Question: LPE error caused by gcRMA [Error in var.M.adap[i] <- ifelse(!is.na(var.M.adap[i - 1]), mean(var.M.adap[i + : replacement has length zero]
0
gravatar for Wolfgang Huber
10.8 years ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k wrote:
Dear Charlie, I agree a lot with you that this is troublesome... but I would be interested in discussing (i) do you (and others) consider this an "error", or rather "bad behaviour" or "poor performance"? (ii) and is it gcrma, or LPE that errs or poorly performs? (iii) and are any of the maintainers of these packages interested in these questions? Best wishes Wolfgang ------------------------------------------------------------------ Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber 31/10/2008 20:05 charliew scripsit > Hi Patrick, > Thanks a lot for the quick reply. I updated the package and it didn't > fix the error. > > c > On Oct 31, 2008, at 3:29 PM, Patrick Aboyoun wrote: > >> Charlie, >> I don't know if this is related to you issue, but a bug in the gcrma >> package was just fixed and there is a version 2.14.1 is now up on >> bioconductor.org. Update to the latest version of gcrma and see if it >> addresses your issue. >> >> >> Patrick >> >> >> >> charliew wrote: >>> Dear List, >>> I've encountered the following error when running LPE: >>> >>> Error in var.M.adap[i] <- ifelse(!is.na(var.M.adap[i - 1]), >>> mean(var.M.adap[i + : >>> replacement has length zero >>> >>> It happens when the CEL files have been processed with gcRMA but not >>> when they have been processed with RMA. >>> I'm not positive about this but I think this error first started >>> happening with the upgrade to gcRMA 2.x >>> I think it is happening because gcRMA is producing a lot of probes >>> with identical expression values. >>> >>> Here is a test session that causes the error. Upon request I can >>> provide a tarball of the test data but any collection of CEL files >>> will reproduce the error. >>> The error also occurs if you run gcRMA from within onecolorGUI or >>> affylmGUI. >>> It also happens if you first write the expression data to a file with >>> write.exprs, then read it back in with read.table. >>> >>> #Loading the packages >>> > library(affy) >>> Loading required package: Biobase >>> Loading required package: tools >>> >>> > library(gcrma) >>> Loading required package: matchprobes >>> Loading required package: splines >>> >>> > library(LPE) >>> > set.seed(0) >>> >>> #Reading in 4 CEL files >>> > test.Dat<-ReadAffy() >>> >>> #Summarizing with gcRMA >>> > test.gcrma<-gcrma(test.Dat) >>> Adjusting for non-specific binding....Done. >>> Normalizing >>> Calculating Expression >>> >>> #Summarizing with RMA >>> > test.rma<-rma(test.Dat) >>> Background correcting >>> Normalizing >>> Calculating Expression >>> >>> #Extracting gcRMA assay data >>> > test.gcrma.MAT<-exprs(test.gcrma) >>> > dim(test.gcrma.MAT) >>> [1] 15611 4 >>> >>> #Extracting RMA assay data >>> >>> > test.rma.MAT<-exprs(test.rma) >>> > dim(test.rma.MAT) >>> [1] 15611 4 >>> >>> #Running LPE function on gcRMA data and the resulting error >>> > var.test.gcrma<-baseOlig.error(test.gcrma.MAT, q= 0.01) >>> Error in var.M.adap[i] <- ifelse(!is.na(var.M.adap[i - 1]), >>> mean(var.M.adap[i + : >>> replacement has length zero >>> >>> #Running LPE function on RMA data - it successfully completes >>> > var.test.rma<-baseOlig.error(test.rma.MAT, q= 0.01) >>> > >>> >>> #My session info >>> > sessionInfo() >>> R version 2.8.0 (2008-10-20) >>> i386-apple-darwin8.11.1 >>> >>> locale: >>> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 >>> >>> attached base packages: >>> [1] splines tools stats graphics grDevices utils >>> datasets methods base >>> >>> other attached packages: >>> [1] xenopuslaevisprobe_2.3.0 xenopuslaeviscdf_2.3.0 >>> LPE_1.16.0 gcrma_2.14.0 >>> matchprobes_1.14.0 affy_1.20.0 Biobase_2.2.0 >>> >>> loaded via a namespace (and not attached): >>> [1] affyio_1.10.0 preprocessCore_1.4.0 >>> >>> Thanks a lot for your help >>> >>> Charlie >>> >>> ------------------------------------------------------------------ ---------- >>> >>> Charlie Whittaker, Ph.D. >>> Bioinformatics and Computing Core Facility >>> The David H. Koch Institute for Integrative Cancer Research At MIT >>> 77 Mass Ave E18-366 >>> Cambridge, MA 02139 >>> >>> 617-324-0337 >>>
cancer gcrma lpe affylmgui • 870 views
ADD COMMENTlink modified 10.8 years ago by Charlie Whittaker70 • written 10.8 years ago by Wolfgang Huber13k
Answer: LPE error caused by gcRMA [Error in var.M.adap[i] <- ifelse(!is.na(var.M.adap[i
0
gravatar for Charlie Whittaker
10.8 years ago by
Charlie Whittaker70 wrote:
Hi Wolfgang, > (i) do you (and others) consider this an "error", or rather "bad > behaviour" or "poor performance"? I'd have to say it is an error because I feel like it should work but it doesn't. Although it is also bad behaviour and poor performance. > (ii) and is it gcrma, or LPE that errs or poorly performs? I don't really know. Both packages can work fine. LPE works great for RMA data or any other data matrices from different array platforms. It just does not work on any gcRMA data that I have tried. gcRMA produces very reasonable summarized data so it seems to work fine too. things break down when I try to take gcRMA data to LPE. I feel like it has something to do with rows that have identical values in all lanes. I think that might be a newer "feature" of gcRMA but I'm not sure. The context of this question is I have a batch of old array data that is being prepped for publication. Back in early 2006 I identified a set of potentially differentially expressed genes by summarizing the data with gcRMA, then diff testing with LPE. Unfortunately I didn't note versions of software and whatnot. Totally my fault. To gather the information I needed to write a good methods section, I wanted to repeat the analysis right now and more carefully document what I did. Trouble is, I get this error out of LPE and that is making it hard to exactly duplicate the old results. One thing I know for sure is the old and new gcRMA data are not identical so that lead me to think that a gcRMA change is the source of the problem. > (iii) and are any of the maintainers of these packages interested in > these questions? hopefully... > Best wishes > Wolfgang > > ------------------------------------------------------------------ > Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber > > > 31/10/2008 20:05 charliew scripsit >> Hi Patrick, >> Thanks a lot for the quick reply. I updated the package and it didn't >> fix the error. >> >> c >> On Oct 31, 2008, at 3:29 PM, Patrick Aboyoun wrote: >> >>> Charlie, >>> I don't know if this is related to you issue, but a bug in the gcrma >>> package was just fixed and there is a version 2.14.1 is now up on >>> bioconductor.org. Update to the latest version of gcrma and see if >>> it >>> addresses your issue. >>> >>> >>> Patrick >>> >>> >>> >>> charliew wrote: >>>> Dear List, >>>> I've encountered the following error when running LPE: >>>> >>>> Error in var.M.adap[i] <- ifelse(!is.na(var.M.adap[i - 1]), >>>> mean(var.M.adap[i + : >>>> replacement has length zero >>>> >>>> It happens when the CEL files have been processed with gcRMA but >>>> not >>>> when they have been processed with RMA. >>>> I'm not positive about this but I think this error first started >>>> happening with the upgrade to gcRMA 2.x >>>> I think it is happening because gcRMA is producing a lot of probes >>>> with identical expression values. >>>> >>>> Here is a test session that causes the error. Upon request I can >>>> provide a tarball of the test data but any collection of CEL files >>>> will reproduce the error. >>>> The error also occurs if you run gcRMA from within onecolorGUI or >>>> affylmGUI. >>>> It also happens if you first write the expression data to a file >>>> with >>>> write.exprs, then read it back in with read.table. >>>> >>>> #Loading the packages >>>>> library(affy) >>>> Loading required package: Biobase >>>> Loading required package: tools >>>> >>>>> library(gcrma) >>>> Loading required package: matchprobes >>>> Loading required package: splines >>>> >>>>> library(LPE) >>>>> set.seed(0) >>>> >>>> #Reading in 4 CEL files >>>>> test.Dat<-ReadAffy() >>>> >>>> #Summarizing with gcRMA >>>>> test.gcrma<-gcrma(test.Dat) >>>> Adjusting for non-specific binding....Done. >>>> Normalizing >>>> Calculating Expression >>>> >>>> #Summarizing with RMA >>>>> test.rma<-rma(test.Dat) >>>> Background correcting >>>> Normalizing >>>> Calculating Expression >>>> >>>> #Extracting gcRMA assay data >>>>> test.gcrma.MAT<-exprs(test.gcrma) >>>>> dim(test.gcrma.MAT) >>>> [1] 15611 4 >>>> >>>> #Extracting RMA assay data >>>> >>>>> test.rma.MAT<-exprs(test.rma) >>>>> dim(test.rma.MAT) >>>> [1] 15611 4 >>>> >>>> #Running LPE function on gcRMA data and the resulting error >>>>> var.test.gcrma<-baseOlig.error(test.gcrma.MAT, q= 0.01) >>>> Error in var.M.adap[i] <- ifelse(!is.na(var.M.adap[i - 1]), >>>> mean(var.M.adap[i + : >>>> replacement has length zero >>>> >>>> #Running LPE function on RMA data - it successfully completes >>>>> var.test.rma<-baseOlig.error(test.rma.MAT, q= 0.01) >>>>> >>>> >>>> #My session info >>>>> sessionInfo() >>>> R version 2.8.0 (2008-10-20) >>>> i386-apple-darwin8.11.1 >>>> >>>> locale: >>>> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 >>>> >>>> attached base packages: >>>> [1] splines tools stats graphics grDevices utils >>>> datasets methods base >>>> >>>> other attached packages: >>>> [1] xenopuslaevisprobe_2.3.0 xenopuslaeviscdf_2.3.0 >>>> LPE_1.16.0 gcrma_2.14.0 >>>> matchprobes_1.14.0 affy_1.20.0 Biobase_2.2.0 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] affyio_1.10.0 preprocessCore_1.4.0 >>>> >>>> Thanks a lot for your help >>>> >>>> Charlie >>>> >>>> ----------------------------------------------------------------- ----------- >>>> >>>> Charlie Whittaker, Ph.D. >>>> Bioinformatics and Computing Core Facility >>>> The David H. Koch Institute for Integrative Cancer Research At MIT >>>> 77 Mass Ave E18-366 >>>> Cambridge, MA 02139 >>>> >>>> 617-324-0337 >>>> >
ADD COMMENTlink written 10.8 years ago by Charlie Whittaker70
Hi, Just to confirm that I and others also observed that since recently GCRMA (>v 2.12) produces identical values for many probesets. See e.g.: http://thread.gmane.org/gmane.science.biology.informatics.conductor/18 84 4/focus=18914 This behaviour is related to a modification in how Gene Specific Background (GSB) is handled in GCRMA v2.12, compared to previous versions. G > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch > [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of charliew > Sent: 04 November 2008 12:12 > To: Wolfgang Huber > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] LPE error caused by gcRMA [Error > invar.M.adap[i] <- ifelse(!is.na(var.M.adap[i - > 1]),mean(var.M.adap[i + : replacement has length zero] > > Hi Wolfgang, > > > (i) do you (and others) consider this an "error", or rather "bad > > behaviour" or "poor performance"? > > I'd have to say it is an error because I feel like it should > work but it doesn't. Although it is also bad behaviour and > poor performance. > > > (ii) and is it gcrma, or LPE that errs or poorly performs? > > I don't really know. Both packages can work fine. > > LPE works great for RMA data or any other data matrices from > different array platforms. It just does not work on any gcRMA > data that I have tried. > > gcRMA produces very reasonable summarized data so it seems to > work fine too. > > things break down when I try to take gcRMA data to LPE. I > feel like it has something to do with rows that have > identical values in all lanes. > I think that might be a newer "feature" of gcRMA but I'm not sure. > > The context of this question is I have a batch of old array > data that is being prepped for publication. > Back in early 2006 I identified a set of potentially > differentially expressed genes by summarizing the data with > gcRMA, then diff testing with LPE. > > Unfortunately I didn't note versions of software and whatnot. > Totally my fault. > > To gather the information I needed to write a good methods > section, I wanted to repeat the analysis right now and more > carefully document what I did. > Trouble is, I get this error out of LPE and that is making it > hard to exactly duplicate the old results. > > One thing I know for sure is the old and new gcRMA data are > not identical so that lead me to think that a gcRMA change is > the source of the problem. > > > (iii) and are any of the maintainers of these packages > interested in > > these questions? > > hopefully... > > > Best wishes > > Wolfgang > > > > ------------------------------------------------------------------ > > Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber > > > > > > 31/10/2008 20:05 charliew scripsit > >> Hi Patrick, > >> Thanks a lot for the quick reply. I updated the package > and it didn't > >> fix the error. > >> > >> c > >> On Oct 31, 2008, at 3:29 PM, Patrick Aboyoun wrote: > >> > >>> Charlie, > >>> I don't know if this is related to you issue, but a bug > in the gcrma > >>> package was just fixed and there is a version 2.14.1 is now up on > >>> bioconductor.org. Update to the latest version of gcrma > and see if > >>> it addresses your issue. > >>> > >>> > >>> Patrick > >>> > >>> > >>> > >>> charliew wrote: > >>>> Dear List, > >>>> I've encountered the following error when running LPE: > >>>> > >>>> Error in var.M.adap[i] <- ifelse(!is.na(var.M.adap[i - 1]), > >>>> mean(var.M.adap[i + : > >>>> replacement has length zero > >>>> > >>>> It happens when the CEL files have been processed with gcRMA but > >>>> not when they have been processed with RMA. > >>>> I'm not positive about this but I think this error first started > >>>> happening with the upgrade to gcRMA 2.x I think it is happening > >>>> because gcRMA is producing a lot of probes with identical > >>>> expression values. > >>>> > >>>> Here is a test session that causes the error. Upon request I can > >>>> provide a tarball of the test data but any collection of > CEL files > >>>> will reproduce the error. > >>>> The error also occurs if you run gcRMA from within > onecolorGUI or > >>>> affylmGUI. > >>>> It also happens if you first write the expression data to a file > >>>> with write.exprs, then read it back in with read.table. > >>>> > >>>> #Loading the packages > >>>>> library(affy) > >>>> Loading required package: Biobase > >>>> Loading required package: tools > >>>> > >>>>> library(gcrma) > >>>> Loading required package: matchprobes Loading required package: > >>>> splines > >>>> > >>>>> library(LPE) > >>>>> set.seed(0) > >>>> > >>>> #Reading in 4 CEL files > >>>>> test.Dat<-ReadAffy() > >>>> > >>>> #Summarizing with gcRMA > >>>>> test.gcrma<-gcrma(test.Dat) > >>>> Adjusting for non-specific binding....Done. > >>>> Normalizing > >>>> Calculating Expression > >>>> > >>>> #Summarizing with RMA > >>>>> test.rma<-rma(test.Dat) > >>>> Background correcting > >>>> Normalizing > >>>> Calculating Expression > >>>> > >>>> #Extracting gcRMA assay data > >>>>> test.gcrma.MAT<-exprs(test.gcrma) > >>>>> dim(test.gcrma.MAT) > >>>> [1] 15611 4 > >>>> > >>>> #Extracting RMA assay data > >>>> > >>>>> test.rma.MAT<-exprs(test.rma) > >>>>> dim(test.rma.MAT) > >>>> [1] 15611 4 > >>>> > >>>> #Running LPE function on gcRMA data and the resulting error > >>>>> var.test.gcrma<-baseOlig.error(test.gcrma.MAT, q= 0.01) > >>>> Error in var.M.adap[i] <- ifelse(!is.na(var.M.adap[i - 1]), > >>>> mean(var.M.adap[i + : > >>>> replacement has length zero > >>>> > >>>> #Running LPE function on RMA data - it successfully completes > >>>>> var.test.rma<-baseOlig.error(test.rma.MAT, q= 0.01) > >>>>> > >>>> > >>>> #My session info > >>>>> sessionInfo() > >>>> R version 2.8.0 (2008-10-20) > >>>> i386-apple-darwin8.11.1 > >>>> > >>>> locale: > >>>> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > >>>> > >>>> attached base packages: > >>>> [1] splines tools stats graphics grDevices utils > >>>> datasets methods base > >>>> > >>>> other attached packages: > >>>> [1] xenopuslaevisprobe_2.3.0 xenopuslaeviscdf_2.3.0 > >>>> LPE_1.16.0 gcrma_2.14.0 > >>>> matchprobes_1.14.0 affy_1.20.0 Biobase_2.2.0 > >>>> > >>>> loaded via a namespace (and not attached): > >>>> [1] affyio_1.10.0 preprocessCore_1.4.0 > >>>> > >>>> Thanks a lot for your help > >>>> > >>>> Charlie > >>>> > >>>> > ------------------------------------------------------------------- > >>>> --------- > >>>> > >>>> Charlie Whittaker, Ph.D. > >>>> Bioinformatics and Computing Core Facility The David H. Koch > >>>> Institute for Integrative Cancer Research At MIT > >>>> 77 Mass Ave E18-366 > >>>> Cambridge, MA 02139 > >>>> > >>>> 617-324-0337 > >>>> > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > >
ADD REPLYlink written 10.8 years ago by Guido Hooiveld2.5k
Charlie Following on from what Guido has said, you could test your hypothesis that the identical values produced by the newer version of gcrma are the problem by adding a small amount of random noise to the gcrma expression values and repeating the LPE analysis. I'm not familiar with LPE myself, but have seen similar problems due to the identical values produced by gcrma with other methods. Best wishes Richard. Hooiveld, Guido wrote: > Hi, > > Just to confirm that I and others also observed that since recently > GCRMA (>v 2.12) produces identical values for many probesets. > See e.g.: > http://thread.gmane.org/gmane.science.biology.informatics.conductor/ 1884 > 4/focus=18914 > This behaviour is related to a modification in how Gene Specific > Background (GSB) is handled in GCRMA v2.12, compared to previous > versions. > > G > >> -----Original Message----- >> From: bioconductor-bounces at stat.math.ethz.ch >> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of charliew >> Sent: 04 November 2008 12:12 >> To: Wolfgang Huber >> Cc: bioconductor at stat.math.ethz.ch >> Subject: Re: [BioC] LPE error caused by gcRMA [Error >> invar.M.adap[i] <- ifelse(!is.na(var.M.adap[i - >> 1]),mean(var.M.adap[i + : replacement has length zero] >> >> Hi Wolfgang, >> >>> (i) do you (and others) consider this an "error", or rather "bad >>> behaviour" or "poor performance"? >> I'd have to say it is an error because I feel like it should >> work but it doesn't. Although it is also bad behaviour and >> poor performance. >> >>> (ii) and is it gcrma, or LPE that errs or poorly performs? >> I don't really know. Both packages can work fine. >> >> LPE works great for RMA data or any other data matrices from >> different array platforms. It just does not work on any gcRMA >> data that I have tried. >> >> gcRMA produces very reasonable summarized data so it seems to >> work fine too. >> >> things break down when I try to take gcRMA data to LPE. I >> feel like it has something to do with rows that have >> identical values in all lanes. >> I think that might be a newer "feature" of gcRMA but I'm not sure. >> >> The context of this question is I have a batch of old array >> data that is being prepped for publication. >> Back in early 2006 I identified a set of potentially >> differentially expressed genes by summarizing the data with >> gcRMA, then diff testing with LPE. >> >> Unfortunately I didn't note versions of software and whatnot. >> Totally my fault. >> >> To gather the information I needed to write a good methods >> section, I wanted to repeat the analysis right now and more >> carefully document what I did. >> Trouble is, I get this error out of LPE and that is making it >> hard to exactly duplicate the old results. >> >> One thing I know for sure is the old and new gcRMA data are >> not identical so that lead me to think that a gcRMA change is >> the source of the problem. >> >>> (iii) and are any of the maintainers of these packages >> interested in >>> these questions? >> hopefully... >> >>> Best wishes >>> Wolfgang >>> >>> ------------------------------------------------------------------ >>> Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber >>> >>> >>> 31/10/2008 20:05 charliew scripsit >>>> Hi Patrick, >>>> Thanks a lot for the quick reply. I updated the package >> and it didn't >>>> fix the error. >>>> >>>> c >>>> On Oct 31, 2008, at 3:29 PM, Patrick Aboyoun wrote: >>>> >>>>> Charlie, >>>>> I don't know if this is related to you issue, but a bug >> in the gcrma >>>>> package was just fixed and there is a version 2.14.1 is now up on >>>>> bioconductor.org. Update to the latest version of gcrma >> and see if >>>>> it addresses your issue. >>>>> >>>>> >>>>> Patrick >>>>> >>>>> >>>>> >>>>> charliew wrote: >>>>>> Dear List, >>>>>> I've encountered the following error when running LPE: >>>>>> >>>>>> Error in var.M.adap[i] <- ifelse(!is.na(var.M.adap[i - 1]), >>>>>> mean(var.M.adap[i + : >>>>>> replacement has length zero >>>>>> >>>>>> It happens when the CEL files have been processed with gcRMA but >>>>>> not when they have been processed with RMA. >>>>>> I'm not positive about this but I think this error first started >>>>>> happening with the upgrade to gcRMA 2.x I think it is happening >>>>>> because gcRMA is producing a lot of probes with identical >>>>>> expression values. >>>>>> >>>>>> Here is a test session that causes the error. Upon request I can >>>>>> provide a tarball of the test data but any collection of >> CEL files >>>>>> will reproduce the error. >>>>>> The error also occurs if you run gcRMA from within >> onecolorGUI or >>>>>> affylmGUI. >>>>>> It also happens if you first write the expression data to a file >>>>>> with write.exprs, then read it back in with read.table. >>>>>> >>>>>> #Loading the packages >>>>>>> library(affy) >>>>>> Loading required package: Biobase >>>>>> Loading required package: tools >>>>>> >>>>>>> library(gcrma) >>>>>> Loading required package: matchprobes Loading required package: >>>>>> splines >>>>>> >>>>>>> library(LPE) >>>>>>> set.seed(0) >>>>>> #Reading in 4 CEL files >>>>>>> test.Dat<-ReadAffy() >>>>>> #Summarizing with gcRMA >>>>>>> test.gcrma<-gcrma(test.Dat) >>>>>> Adjusting for non-specific binding....Done. >>>>>> Normalizing >>>>>> Calculating Expression >>>>>> >>>>>> #Summarizing with RMA >>>>>>> test.rma<-rma(test.Dat) >>>>>> Background correcting >>>>>> Normalizing >>>>>> Calculating Expression >>>>>> >>>>>> #Extracting gcRMA assay data >>>>>>> test.gcrma.MAT<-exprs(test.gcrma) >>>>>>> dim(test.gcrma.MAT) >>>>>> [1] 15611 4 >>>>>> >>>>>> #Extracting RMA assay data >>>>>> >>>>>>> test.rma.MAT<-exprs(test.rma) >>>>>>> dim(test.rma.MAT) >>>>>> [1] 15611 4 >>>>>> >>>>>> #Running LPE function on gcRMA data and the resulting error >>>>>>> var.test.gcrma<-baseOlig.error(test.gcrma.MAT, q= 0.01) >>>>>> Error in var.M.adap[i] <- ifelse(!is.na(var.M.adap[i - 1]), >>>>>> mean(var.M.adap[i + : >>>>>> replacement has length zero >>>>>> >>>>>> #Running LPE function on RMA data - it successfully completes >>>>>>> var.test.rma<-baseOlig.error(test.rma.MAT, q= 0.01) >>>>>>> >>>>>> #My session info >>>>>>> sessionInfo() >>>>>> R version 2.8.0 (2008-10-20) >>>>>> i386-apple-darwin8.11.1 >>>>>> >>>>>> locale: >>>>>> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 >>>>>> >>>>>> attached base packages: >>>>>> [1] splines tools stats graphics grDevices utils >>>>>> datasets methods base >>>>>> >>>>>> other attached packages: >>>>>> [1] xenopuslaevisprobe_2.3.0 xenopuslaeviscdf_2.3.0 >>>>>> LPE_1.16.0 gcrma_2.14.0 >>>>>> matchprobes_1.14.0 affy_1.20.0 Biobase_2.2.0 >>>>>> >>>>>> loaded via a namespace (and not attached): >>>>>> [1] affyio_1.10.0 preprocessCore_1.4.0 >>>>>> >>>>>> Thanks a lot for your help >>>>>> >>>>>> Charlie >>>>>> >>>>>> >> ------------------------------------------------------------------- >>>>>> --------- >>>>>> >>>>>> Charlie Whittaker, Ph.D. >>>>>> Bioinformatics and Computing Core Facility The David H. Koch >>>>>> Institute for Integrative Cancer Research At MIT >>>>>> 77 Mass Ave E18-366 >>>>>> Cambridge, MA 02139 >>>>>> >>>>>> 617-324-0337 >>>>>> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Richard D. Pearson richard.pearson at postgrad.manchester.ac.uk School of Computer Science, http://www.cs.man.ac.uk/~pearsonr University of Manchester, Tel: +44 161 275 6178 Oxford Road, Mob: +44 7971 221181 Manchester M13 9PL, UK. Fax: +44 161 275 6204
ADD REPLYlink written 10.8 years ago by Richard Pearson390
04/11/2008 12:48 Richard Pearson scripsit > Charlie > > Following on from what Guido has said, you could test your hypothesis > that the identical values produced by the newer version of gcrma are the > problem by adding a small amount of random noise to the gcrma expression > values and repeating the LPE analysis. I'm not familiar with LPE myself, > but have seen similar problems due to the identical values produced by > gcrma with other methods. > Wait a minute ... the raw intensities of one probe vary randomly across arrays. Most normalisation methods remove some of this variation (the systematic part), while some remains. Now we have a method that -for some probes- totally removes this variation, and provides identical estimates across arrays. Simply adding artificial noise (from which distribution?) won't solve any real problem. Best wishes Wolfgang ------------------------------------------------------------------ Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber > Best wishes > > Richard. > > Hooiveld, Guido wrote: >> Hi, >> >> Just to confirm that I and others also observed that since recently >> GCRMA (>v 2.12) produces identical values for many probesets. >> See e.g.: >> http://thread.gmane.org/gmane.science.biology.informatics.conductor /1884 >> 4/focus=18914 >> This behaviour is related to a modification in how Gene Specific >> Background (GSB) is handled in GCRMA v2.12, compared to previous >> versions. >> >> G >>> -----Original Message----- >>> From: bioconductor-bounces at stat.math.ethz.ch >>> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of charliew >>> Sent: 04 November 2008 12:12 >>> To: Wolfgang Huber >>> Cc: bioconductor at stat.math.ethz.ch >>> Subject: Re: [BioC] LPE error caused by gcRMA [Error invar.M.adap[i] >>> <- ifelse(!is.na(var.M.adap[i - 1]),mean(var.M.adap[i + : replacement >>> has length zero] >>> >>> Hi Wolfgang, >>> >>>> (i) do you (and others) consider this an "error", or rather "bad >>>> behaviour" or "poor performance"? >>> I'd have to say it is an error because I feel like it should work but >>> it doesn't. Although it is also bad behaviour and poor performance. >>> >>>> (ii) and is it gcrma, or LPE that errs or poorly performs? >>> I don't really know. Both packages can work fine. >>> >>> LPE works great for RMA data or any other data matrices from >>> different array platforms. It just does not work on any gcRMA data >>> that I have tried. >>> >>> gcRMA produces very reasonable summarized data so it seems to work >>> fine too. >>> >>> things break down when I try to take gcRMA data to LPE. I feel like >>> it has something to do with rows that have identical values in all >>> lanes. >>> I think that might be a newer "feature" of gcRMA but I'm not sure. >>> >>> The context of this question is I have a batch of old array data that >>> is being prepped for publication. >>> Back in early 2006 I identified a set of potentially differentially >>> expressed genes by summarizing the data with gcRMA, then diff testing >>> with LPE. >>> >>> Unfortunately I didn't note versions of software and whatnot. Totally >>> my fault. >>> >>> To gather the information I needed to write a good methods section, I >>> wanted to repeat the analysis right now and more carefully document >>> what I did. >>> Trouble is, I get this error out of LPE and that is making it hard to >>> exactly duplicate the old results. >>> >>> One thing I know for sure is the old and new gcRMA data are not >>> identical so that lead me to think that a gcRMA change is the source >>> of the problem. >>> >>>> (iii) and are any of the maintainers of these packages >>> interested in >>>> these questions? >>> hopefully... >>> >>>> Best wishes >>>> Wolfgang >>>> >>>> ------------------------------------------------------------------ >>>> Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber >>>> >>>> >>>> 31/10/2008 20:05 charliew scripsit >>>>> Hi Patrick, >>>>> Thanks a lot for the quick reply. I updated the package >>> and it didn't >>>>> fix the error. >>>>> >>>>> c >>>>> On Oct 31, 2008, at 3:29 PM, Patrick Aboyoun wrote: >>>>> >>>>>> Charlie, >>>>>> I don't know if this is related to you issue, but a bug >>> in the gcrma >>>>>> package was just fixed and there is a version 2.14.1 is now up on >>>>>> bioconductor.org. Update to the latest version of gcrma >>> and see if >>>>>> it addresses your issue. >>>>>> >>>>>> >>>>>> Patrick >>>>>> >>>>>> >>>>>> >>>>>> charliew wrote: >>>>>>> Dear List, >>>>>>> I've encountered the following error when running LPE: >>>>>>> >>>>>>> Error in var.M.adap[i] <- ifelse(!is.na(var.M.adap[i - 1]), >>>>>>> mean(var.M.adap[i + : >>>>>>> replacement has length zero >>>>>>> >>>>>>> It happens when the CEL files have been processed with gcRMA but >>>>>>> not when they have been processed with RMA. >>>>>>> I'm not positive about this but I think this error first started >>>>>>> happening with the upgrade to gcRMA 2.x I think it is happening >>>>>>> because gcRMA is producing a lot of probes with identical >>>>>>> expression values. >>>>>>> >>>>>>> Here is a test session that causes the error. Upon request I can >>>>>>> provide a tarball of the test data but any collection of >>> CEL files >>>>>>> will reproduce the error. >>>>>>> The error also occurs if you run gcRMA from within >>> onecolorGUI or >>>>>>> affylmGUI. >>>>>>> It also happens if you first write the expression data to a file >>>>>>> with write.exprs, then read it back in with read.table. >>>>>>> >>>>>>> #Loading the packages >>>>>>>> library(affy) >>>>>>> Loading required package: Biobase >>>>>>> Loading required package: tools >>>>>>> >>>>>>>> library(gcrma) >>>>>>> Loading required package: matchprobes Loading required package: >>>>>>> splines >>>>>>> >>>>>>>> library(LPE) >>>>>>>> set.seed(0) >>>>>>> #Reading in 4 CEL files >>>>>>>> test.Dat<-ReadAffy() >>>>>>> #Summarizing with gcRMA >>>>>>>> test.gcrma<-gcrma(test.Dat) >>>>>>> Adjusting for non-specific binding....Done. >>>>>>> Normalizing >>>>>>> Calculating Expression >>>>>>> >>>>>>> #Summarizing with RMA >>>>>>>> test.rma<-rma(test.Dat) >>>>>>> Background correcting >>>>>>> Normalizing >>>>>>> Calculating Expression >>>>>>> >>>>>>> #Extracting gcRMA assay data >>>>>>>> test.gcrma.MAT<-exprs(test.gcrma) >>>>>>>> dim(test.gcrma.MAT) >>>>>>> [1] 15611 4 >>>>>>> >>>>>>> #Extracting RMA assay data >>>>>>> >>>>>>>> test.rma.MAT<-exprs(test.rma) >>>>>>>> dim(test.rma.MAT) >>>>>>> [1] 15611 4 >>>>>>> >>>>>>> #Running LPE function on gcRMA data and the resulting error >>>>>>>> var.test.gcrma<-baseOlig.error(test.gcrma.MAT, q= 0.01) >>>>>>> Error in var.M.adap[i] <- ifelse(!is.na(var.M.adap[i - 1]), >>>>>>> mean(var.M.adap[i + : >>>>>>> replacement has length zero >>>>>>> >>>>>>> #Running LPE function on RMA data - it successfully completes >>>>>>>> var.test.rma<-baseOlig.error(test.rma.MAT, q= 0.01) >>>>>>>> >>>>>>> #My session info >>>>>>>> sessionInfo() >>>>>>> R version 2.8.0 (2008-10-20) >>>>>>> i386-apple-darwin8.11.1 >>>>>>> >>>>>>> locale: >>>>>>> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 >>>>>>> >>>>>>> attached base packages: >>>>>>> [1] splines tools stats graphics grDevices utils >>>>>>> datasets methods base >>>>>>> >>>>>>> other attached packages: >>>>>>> [1] xenopuslaevisprobe_2.3.0 xenopuslaeviscdf_2.3.0 >>>>>>> LPE_1.16.0 gcrma_2.14.0 >>>>>>> matchprobes_1.14.0 affy_1.20.0 Biobase_2.2.0 >>>>>>> >>>>>>> loaded via a namespace (and not attached): >>>>>>> [1] affyio_1.10.0 preprocessCore_1.4.0 >>>>>>> >>>>>>> Thanks a lot for your help >>>>>>> >>>>>>> Charlie >>>>>>> >>>>>>> >>> ------------------------------------------------------------------- >>>>>>> --------- >>>>>>> >>>>>>> Charlie Whittaker, Ph.D. >>>>>>> Bioinformatics and Computing Core Facility The David H. Koch >>>>>>> Institute for Integrative Cancer Research At MIT >>>>>>> 77 Mass Ave E18-366 >>>>>>> Cambridge, MA 02139 >>>>>>> >>>>>>> 617-324-0337 >>>>>>>
ADD REPLYlink written 10.8 years ago by Wolfgang Huber13k
Wolfgang I agree with you completely. I'm not suggesting adding random noise will remove any real problem, I'm just suggesting Charlie could do this to see whether his hypothesis about the equal values causing the problem is correct. Personally I think adding random noise should be avoided in any real analysis. Richard. Wolfgang Huber wrote: > > > 04/11/2008 12:48 Richard Pearson scripsit >> Charlie >> >> Following on from what Guido has said, you could test your hypothesis >> that the identical values produced by the newer version of gcrma are the >> problem by adding a small amount of random noise to the gcrma expression >> values and repeating the LPE analysis. I'm not familiar with LPE myself, >> but have seen similar problems due to the identical values produced by >> gcrma with other methods. >> > > > Wait a minute ... the raw intensities of one probe vary randomly across > arrays. Most normalisation methods remove some of this variation (the > systematic part), while some remains. Now we have a method that -for > some probes- totally removes this variation, and provides identical > estimates across arrays. > > Simply adding artificial noise (from which distribution?) won't solve > any real problem. > > Best wishes > Wolfgang > > ------------------------------------------------------------------ > Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber > > > >> Best wishes >> >> Richard. >> >> Hooiveld, Guido wrote: >>> Hi, >>> >>> Just to confirm that I and others also observed that since recently >>> GCRMA (>v 2.12) produces identical values for many probesets. >>> See e.g.: >>> http://thread.gmane.org/gmane.science.biology.informatics.conducto r/1884 >>> 4/focus=18914 >>> This behaviour is related to a modification in how Gene Specific >>> Background (GSB) is handled in GCRMA v2.12, compared to previous >>> versions. >>> >>> G >>>> -----Original Message----- >>>> From: bioconductor-bounces at stat.math.ethz.ch >>>> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of charliew >>>> Sent: 04 November 2008 12:12 >>>> To: Wolfgang Huber >>>> Cc: bioconductor at stat.math.ethz.ch >>>> Subject: Re: [BioC] LPE error caused by gcRMA [Error invar.M.adap[i] >>>> <- ifelse(!is.na(var.M.adap[i - 1]),mean(var.M.adap[i + : replacement >>>> has length zero] >>>> >>>> Hi Wolfgang, >>>> >>>>> (i) do you (and others) consider this an "error", or rather "bad >>>>> behaviour" or "poor performance"? >>>> I'd have to say it is an error because I feel like it should work but >>>> it doesn't. Although it is also bad behaviour and poor performance. >>>> >>>>> (ii) and is it gcrma, or LPE that errs or poorly performs? >>>> I don't really know. Both packages can work fine. >>>> >>>> LPE works great for RMA data or any other data matrices from >>>> different array platforms. It just does not work on any gcRMA data >>>> that I have tried. >>>> >>>> gcRMA produces very reasonable summarized data so it seems to work >>>> fine too. >>>> >>>> things break down when I try to take gcRMA data to LPE. I feel like >>>> it has something to do with rows that have identical values in all >>>> lanes. >>>> I think that might be a newer "feature" of gcRMA but I'm not sure. >>>> >>>> The context of this question is I have a batch of old array data that >>>> is being prepped for publication. >>>> Back in early 2006 I identified a set of potentially differentially >>>> expressed genes by summarizing the data with gcRMA, then diff testing >>>> with LPE. >>>> >>>> Unfortunately I didn't note versions of software and whatnot. Totally >>>> my fault. >>>> >>>> To gather the information I needed to write a good methods section, I >>>> wanted to repeat the analysis right now and more carefully document >>>> what I did. >>>> Trouble is, I get this error out of LPE and that is making it hard to >>>> exactly duplicate the old results. >>>> >>>> One thing I know for sure is the old and new gcRMA data are not >>>> identical so that lead me to think that a gcRMA change is the source >>>> of the problem. >>>> >>>>> (iii) and are any of the maintainers of these packages >>>> interested in >>>>> these questions? >>>> hopefully... >>>> >>>>> Best wishes >>>>> Wolfgang >>>>> >>>>> ------------------------------------------------------------------ >>>>> Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber >>>>> >>>>> >>>>> 31/10/2008 20:05 charliew scripsit >>>>>> Hi Patrick, >>>>>> Thanks a lot for the quick reply. I updated the package >>>> and it didn't >>>>>> fix the error. >>>>>> >>>>>> c >>>>>> On Oct 31, 2008, at 3:29 PM, Patrick Aboyoun wrote: >>>>>> >>>>>>> Charlie, >>>>>>> I don't know if this is related to you issue, but a bug >>>> in the gcrma >>>>>>> package was just fixed and there is a version 2.14.1 is now up on >>>>>>> bioconductor.org. Update to the latest version of gcrma >>>> and see if >>>>>>> it addresses your issue. >>>>>>> >>>>>>> >>>>>>> Patrick >>>>>>> >>>>>>> >>>>>>> >>>>>>> charliew wrote: >>>>>>>> Dear List, >>>>>>>> I've encountered the following error when running LPE: >>>>>>>> >>>>>>>> Error in var.M.adap[i] <- ifelse(!is.na(var.M.adap[i - 1]), >>>>>>>> mean(var.M.adap[i + : >>>>>>>> replacement has length zero >>>>>>>> >>>>>>>> It happens when the CEL files have been processed with gcRMA but >>>>>>>> not when they have been processed with RMA. >>>>>>>> I'm not positive about this but I think this error first started >>>>>>>> happening with the upgrade to gcRMA 2.x I think it is happening >>>>>>>> because gcRMA is producing a lot of probes with identical >>>>>>>> expression values. >>>>>>>> >>>>>>>> Here is a test session that causes the error. Upon request I can >>>>>>>> provide a tarball of the test data but any collection of >>>> CEL files >>>>>>>> will reproduce the error. >>>>>>>> The error also occurs if you run gcRMA from within >>>> onecolorGUI or >>>>>>>> affylmGUI. >>>>>>>> It also happens if you first write the expression data to a file >>>>>>>> with write.exprs, then read it back in with read.table. >>>>>>>> >>>>>>>> #Loading the packages >>>>>>>>> library(affy) >>>>>>>> Loading required package: Biobase >>>>>>>> Loading required package: tools >>>>>>>> >>>>>>>>> library(gcrma) >>>>>>>> Loading required package: matchprobes Loading required package: >>>>>>>> splines >>>>>>>> >>>>>>>>> library(LPE) >>>>>>>>> set.seed(0) >>>>>>>> #Reading in 4 CEL files >>>>>>>>> test.Dat<-ReadAffy() >>>>>>>> #Summarizing with gcRMA >>>>>>>>> test.gcrma<-gcrma(test.Dat) >>>>>>>> Adjusting for non-specific binding....Done. >>>>>>>> Normalizing >>>>>>>> Calculating Expression >>>>>>>> >>>>>>>> #Summarizing with RMA >>>>>>>>> test.rma<-rma(test.Dat) >>>>>>>> Background correcting >>>>>>>> Normalizing >>>>>>>> Calculating Expression >>>>>>>> >>>>>>>> #Extracting gcRMA assay data >>>>>>>>> test.gcrma.MAT<-exprs(test.gcrma) >>>>>>>>> dim(test.gcrma.MAT) >>>>>>>> [1] 15611 4 >>>>>>>> >>>>>>>> #Extracting RMA assay data >>>>>>>> >>>>>>>>> test.rma.MAT<-exprs(test.rma) >>>>>>>>> dim(test.rma.MAT) >>>>>>>> [1] 15611 4 >>>>>>>> >>>>>>>> #Running LPE function on gcRMA data and the resulting error >>>>>>>>> var.test.gcrma<-baseOlig.error(test.gcrma.MAT, q= 0.01) >>>>>>>> Error in var.M.adap[i] <- ifelse(!is.na(var.M.adap[i - 1]), >>>>>>>> mean(var.M.adap[i + : >>>>>>>> replacement has length zero >>>>>>>> >>>>>>>> #Running LPE function on RMA data - it successfully completes >>>>>>>>> var.test.rma<-baseOlig.error(test.rma.MAT, q= 0.01) >>>>>>>>> >>>>>>>> #My session info >>>>>>>>> sessionInfo() >>>>>>>> R version 2.8.0 (2008-10-20) >>>>>>>> i386-apple-darwin8.11.1 >>>>>>>> >>>>>>>> locale: >>>>>>>> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 >>>>>>>> >>>>>>>> attached base packages: >>>>>>>> [1] splines tools stats graphics grDevices utils >>>>>>>> datasets methods base >>>>>>>> >>>>>>>> other attached packages: >>>>>>>> [1] xenopuslaevisprobe_2.3.0 xenopuslaeviscdf_2.3.0 >>>>>>>> LPE_1.16.0 gcrma_2.14.0 >>>>>>>> matchprobes_1.14.0 affy_1.20.0 Biobase_2.2.0 >>>>>>>> >>>>>>>> loaded via a namespace (and not attached): >>>>>>>> [1] affyio_1.10.0 preprocessCore_1.4.0 >>>>>>>> >>>>>>>> Thanks a lot for your help >>>>>>>> >>>>>>>> Charlie >>>>>>>> >>>>>>>> >>>> ------------------------------------------------------------------- >>>>>>>> --------- >>>>>>>> >>>>>>>> Charlie Whittaker, Ph.D. >>>>>>>> Bioinformatics and Computing Core Facility The David H. Koch >>>>>>>> Institute for Integrative Cancer Research At MIT >>>>>>>> 77 Mass Ave E18-366 >>>>>>>> Cambridge, MA 02139 >>>>>>>> >>>>>>>> 617-324-0337 >>>>>>>> > -- Richard D. Pearson richard.pearson at postgrad.manchester.ac.uk School of Computer Science, http://www.cs.man.ac.uk/~pearsonr University of Manchester, Tel: +44 161 275 6178 Oxford Road, Mob: +44 7971 221181 Manchester M13 9PL, UK. Fax: +44 161 275 6204
ADD REPLYlink written 10.8 years ago by Richard Pearson390
Hi Richard, The error went away when I added a small random number to every value in the data and re-ran LPE. charlie On Nov 5, 2008, at 5:57 AM, Richard Pearson wrote: > Wolfgang > > I agree with you completely. I'm not suggesting adding random noise > will remove any real problem, I'm just suggesting Charlie could do > this to see whether his hypothesis about the equal values causing > the problem is correct. Personally I think adding random noise > should be avoided in any real analysis. > > Richard. > > > Wolfgang Huber wrote: >> 04/11/2008 12:48 Richard Pearson scripsit >>> Charlie >>> >>> Following on from what Guido has said, you could test your >>> hypothesis >>> that the identical values produced by the newer version of gcrma >>> are the >>> problem by adding a small amount of random noise to the gcrma >>> expression >>> values and repeating the LPE analysis. I'm not familiar with LPE >>> myself, >>> but have seen similar problems due to the identical values >>> produced by >>> gcrma with other methods. >>> >> Wait a minute ... the raw intensities of one probe vary randomly >> across >> arrays. Most normalisation methods remove some of this variation (the >> systematic part), while some remains. Now we have a method that -for >> some probes- totally removes this variation, and provides identical >> estimates across arrays. >> Simply adding artificial noise (from which distribution?) won't solve >> any real problem. >> Best wishes >> Wolfgang >> ------------------------------------------------------------------ >> ---------------------------------------------------------------------- ------ Charlie Whittaker, Ph.D. Bioinformatics and Computing Core Facility The David H. Koch Institute for Integrative Cancer Research At MIT 77 Mass Ave E18-366 Cambridge, MA 02139 617-324-0337
ADD REPLYlink written 10.8 years ago by Charlie Whittaker70
I also did gcrma (and maanova) in 2006 and did not write down version numbers (stupid me), and now am processing the data Is there a page where version numbers of packages are listed by date? > From: "Hooiveld, Guido" <guido.hooiveld at="" wur.nl=""> > Date: Tue, 4 Nov 2008 12:51:30 +0100 > To: charliew <charliew at="" mit.edu="">, Wolfgang Huber <huber at="" ebi.ac.uk=""> > Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch=""> > Subject: Re: [BioC] LPE error caused by gcRMA [Error invar.M.adap[i] <- > ifelse(!is.na(var.M.adap[i - 1]), mean(var.M.adap[i + : replacement has length > zero] > > > Hi, > > Just to confirm that I and others also observed that since recently > GCRMA (>v 2.12) produces identical values for many probesets. > See e.g.: > http://thread.gmane.org/gmane.science.biology.informatics.conductor/ 1884 > 4/focus=18914 > This behaviour is related to a modification in how Gene Specific > Background (GSB) is handled in GCRMA v2.12, compared to previous > versions. > > G > >> -----Original Message----- >> From: bioconductor-bounces at stat.math.ethz.ch >> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of charliew >> Sent: 04 November 2008 12:12 >> To: Wolfgang Huber >> Cc: bioconductor at stat.math.ethz.ch >> Subject: Re: [BioC] LPE error caused by gcRMA [Error >> invar.M.adap[i] <- ifelse(!is.na(var.M.adap[i - >> 1]),mean(var.M.adap[i + : replacement has length zero] >> >> Hi Wolfgang, >> >>> (i) do you (and others) consider this an "error", or rather "bad >>> behaviour" or "poor performance"? >> >> I'd have to say it is an error because I feel like it should >> work but it doesn't. Although it is also bad behaviour and >> poor performance. >> >>> (ii) and is it gcrma, or LPE that errs or poorly performs? >> >> I don't really know. Both packages can work fine. >> >> LPE works great for RMA data or any other data matrices from >> different array platforms. It just does not work on any gcRMA >> data that I have tried. >> >> gcRMA produces very reasonable summarized data so it seems to >> work fine too. >> >> things break down when I try to take gcRMA data to LPE. I >> feel like it has something to do with rows that have >> identical values in all lanes. >> I think that might be a newer "feature" of gcRMA but I'm not sure. >> >> The context of this question is I have a batch of old array >> data that is being prepped for publication. >> Back in early 2006 I identified a set of potentially >> differentially expressed genes by summarizing the data with >> gcRMA, then diff testing with LPE. >> >> Unfortunately I didn't note versions of software and whatnot. >> Totally my fault. >> >> To gather the information I needed to write a good methods >> section, I wanted to repeat the analysis right now and more >> carefully document what I did. >> Trouble is, I get this error out of LPE and that is making it >> hard to exactly duplicate the old results. >> >> One thing I know for sure is the old and new gcRMA data are >> not identical so that lead me to think that a gcRMA change is >> the source of the problem. >> >>> (iii) and are any of the maintainers of these packages >> interested in >>> these questions? >> >> hopefully... >> >>> Best wishes >>> Wolfgang >>> >>> ------------------------------------------------------------------ >>> Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber >>> >>> >>> 31/10/2008 20:05 charliew scripsit >>>> Hi Patrick, >>>> Thanks a lot for the quick reply. I updated the package >> and it didn't >>>> fix the error. >>>> >>>> c >>>> On Oct 31, 2008, at 3:29 PM, Patrick Aboyoun wrote: >>>> >>>>> Charlie, >>>>> I don't know if this is related to you issue, but a bug >> in the gcrma >>>>> package was just fixed and there is a version 2.14.1 is now up on >>>>> bioconductor.org. Update to the latest version of gcrma >> and see if >>>>> it addresses your issue. >>>>> >>>>> >>>>> Patrick >>>>> >>>>> >>>>> >>>>> charliew wrote: >>>>>> Dear List, >>>>>> I've encountered the following error when running LPE: >>>>>> >>>>>> Error in var.M.adap[i] <- ifelse(!is.na(var.M.adap[i - 1]), >>>>>> mean(var.M.adap[i + : >>>>>> replacement has length zero >>>>>> >>>>>> It happens when the CEL files have been processed with gcRMA but >>>>>> not when they have been processed with RMA. >>>>>> I'm not positive about this but I think this error first started >>>>>> happening with the upgrade to gcRMA 2.x I think it is happening >>>>>> because gcRMA is producing a lot of probes with identical >>>>>> expression values. >>>>>> >>>>>> Here is a test session that causes the error. Upon request I can >>>>>> provide a tarball of the test data but any collection of >> CEL files >>>>>> will reproduce the error. >>>>>> The error also occurs if you run gcRMA from within >> onecolorGUI or >>>>>> affylmGUI. >>>>>> It also happens if you first write the expression data to a file >>>>>> with write.exprs, then read it back in with read.table. >>>>>> >>>>>> #Loading the packages >>>>>>> library(affy) >>>>>> Loading required package: Biobase >>>>>> Loading required package: tools >>>>>> >>>>>>> library(gcrma) >>>>>> Loading required package: matchprobes Loading required package: >>>>>> splines >>>>>> >>>>>>> library(LPE) >>>>>>> set.seed(0) >>>>>> >>>>>> #Reading in 4 CEL files >>>>>>> test.Dat<-ReadAffy() >>>>>> >>>>>> #Summarizing with gcRMA >>>>>>> test.gcrma<-gcrma(test.Dat) >>>>>> Adjusting for non-specific binding....Done. >>>>>> Normalizing >>>>>> Calculating Expression >>>>>> >>>>>> #Summarizing with RMA >>>>>>> test.rma<-rma(test.Dat) >>>>>> Background correcting >>>>>> Normalizing >>>>>> Calculating Expression >>>>>> >>>>>> #Extracting gcRMA assay data >>>>>>> test.gcrma.MAT<-exprs(test.gcrma) >>>>>>> dim(test.gcrma.MAT) >>>>>> [1] 15611 4 >>>>>> >>>>>> #Extracting RMA assay data >>>>>> >>>>>>> test.rma.MAT<-exprs(test.rma) >>>>>>> dim(test.rma.MAT) >>>>>> [1] 15611 4 >>>>>> >>>>>> #Running LPE function on gcRMA data and the resulting error >>>>>>> var.test.gcrma<-baseOlig.error(test.gcrma.MAT, q= 0.01) >>>>>> Error in var.M.adap[i] <- ifelse(!is.na(var.M.adap[i - 1]), >>>>>> mean(var.M.adap[i + : >>>>>> replacement has length zero >>>>>> >>>>>> #Running LPE function on RMA data - it successfully completes >>>>>>> var.test.rma<-baseOlig.error(test.rma.MAT, q= 0.01) >>>>>>> >>>>>> >>>>>> #My session info >>>>>>> sessionInfo() >>>>>> R version 2.8.0 (2008-10-20) >>>>>> i386-apple-darwin8.11.1 >>>>>> >>>>>> locale: >>>>>> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 >>>>>> >>>>>> attached base packages: >>>>>> [1] splines tools stats graphics grDevices utils >>>>>> datasets methods base >>>>>> >>>>>> other attached packages: >>>>>> [1] xenopuslaevisprobe_2.3.0 xenopuslaeviscdf_2.3.0 >>>>>> LPE_1.16.0 gcrma_2.14.0 >>>>>> matchprobes_1.14.0 affy_1.20.0 Biobase_2.2.0 >>>>>> >>>>>> loaded via a namespace (and not attached): >>>>>> [1] affyio_1.10.0 preprocessCore_1.4.0 >>>>>> >>>>>> Thanks a lot for your help >>>>>> >>>>>> Charlie >>>>>> >>>>>> >> ------------------------------------------------------------------- >>>>>> --------- >>>>>> >>>>>> Charlie Whittaker, Ph.D. >>>>>> Bioinformatics and Computing Core Facility The David H. Koch >>>>>> Institute for Integrative Cancer Research At MIT >>>>>> 77 Mass Ave E18-366 >>>>>> Cambridge, MA 02139 >>>>>> >>>>>> 617-324-0337 >>>>>> >>> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLYlink written 10.8 years ago by Loren Engrav1.0k
On Tue, 2008-11-04 at 20:12 -0800, Loren Engrav wrote: > I also did gcrma (and maanova) in 2006 and did not write down version > numbers (stupid me), and now am processing the data > > Is there a page where version numbers of packages are listed by date? > The VCS records all changes by date, and the file DESCRIPTION will contain the package version number change. svn log gcrma/DESCRIPTION Look for the word 'release' or 'version' and note the revision numbers you are interested in and: svn diff -r<revision number=""> gcrma/DESCRIPTION | grep Version L. > > > > From: "Hooiveld, Guido" <guido.hooiveld at="" wur.nl=""> > > Date: Tue, 4 Nov 2008 12:51:30 +0100 > > To: charliew <charliew at="" mit.edu="">, Wolfgang Huber <huber at="" ebi.ac.uk=""> > > Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch=""> > > Subject: Re: [BioC] LPE error caused by gcRMA [Error invar.M.adap[i] <- > > ifelse(!is.na(var.M.adap[i - 1]), mean(var.M.adap[i + : replacement has length > > zero] > > > > > > Hi, > > > > Just to confirm that I and others also observed that since recently > > GCRMA (>v 2.12) produces identical values for many probesets. > > See e.g.: > > http://thread.gmane.org/gmane.science.biology.informatics.conducto r/1884 > > 4/focus=18914 > > This behaviour is related to a modification in how Gene Specific > > Background (GSB) is handled in GCRMA v2.12, compared to previous > > versions. > > > > G > > > >> -----Original Message----- > >> From: bioconductor-bounces at stat.math.ethz.ch > >> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of charliew > >> Sent: 04 November 2008 12:12 > >> To: Wolfgang Huber > >> Cc: bioconductor at stat.math.ethz.ch > >> Subject: Re: [BioC] LPE error caused by gcRMA [Error > >> invar.M.adap[i] <- ifelse(!is.na(var.M.adap[i - > >> 1]),mean(var.M.adap[i + : replacement has length zero] > >> > >> Hi Wolfgang, > >> > >>> (i) do you (and others) consider this an "error", or rather "bad > >>> behaviour" or "poor performance"? > >> > >> I'd have to say it is an error because I feel like it should > >> work but it doesn't. Although it is also bad behaviour and > >> poor performance. > >> > >>> (ii) and is it gcrma, or LPE that errs or poorly performs? > >> > >> I don't really know. Both packages can work fine. > >> > >> LPE works great for RMA data or any other data matrices from > >> different array platforms. It just does not work on any gcRMA > >> data that I have tried. > >> > >> gcRMA produces very reasonable summarized data so it seems to > >> work fine too. > >> > >> things break down when I try to take gcRMA data to LPE. I > >> feel like it has something to do with rows that have > >> identical values in all lanes. > >> I think that might be a newer "feature" of gcRMA but I'm not sure. > >> > >> The context of this question is I have a batch of old array > >> data that is being prepped for publication. > >> Back in early 2006 I identified a set of potentially > >> differentially expressed genes by summarizing the data with > >> gcRMA, then diff testing with LPE. > >> > >> Unfortunately I didn't note versions of software and whatnot. > >> Totally my fault. > >> > >> To gather the information I needed to write a good methods > >> section, I wanted to repeat the analysis right now and more > >> carefully document what I did. > >> Trouble is, I get this error out of LPE and that is making it > >> hard to exactly duplicate the old results. > >> > >> One thing I know for sure is the old and new gcRMA data are > >> not identical so that lead me to think that a gcRMA change is > >> the source of the problem. > >> > >>> (iii) and are any of the maintainers of these packages > >> interested in > >>> these questions? > >> > >> hopefully... > >> > >>> Best wishes > >>> Wolfgang > >>> > >>> ------------------------------------------------------------------ > >>> Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber > >>> > >>> > >>> 31/10/2008 20:05 charliew scripsit > >>>> Hi Patrick, > >>>> Thanks a lot for the quick reply. I updated the package > >> and it didn't > >>>> fix the error. > >>>> > >>>> c > >>>> On Oct 31, 2008, at 3:29 PM, Patrick Aboyoun wrote: > >>>> > >>>>> Charlie, > >>>>> I don't know if this is related to you issue, but a bug > >> in the gcrma > >>>>> package was just fixed and there is a version 2.14.1 is now up on > >>>>> bioconductor.org. Update to the latest version of gcrma > >> and see if > >>>>> it addresses your issue. > >>>>> > >>>>> > >>>>> Patrick > >>>>> > >>>>> > >>>>> > >>>>> charliew wrote: > >>>>>> Dear List, > >>>>>> I've encountered the following error when running LPE: > >>>>>> > >>>>>> Error in var.M.adap[i] <- ifelse(!is.na(var.M.adap[i - 1]), > >>>>>> mean(var.M.adap[i + : > >>>>>> replacement has length zero > >>>>>> > >>>>>> It happens when the CEL files have been processed with gcRMA but > >>>>>> not when they have been processed with RMA. > >>>>>> I'm not positive about this but I think this error first started > >>>>>> happening with the upgrade to gcRMA 2.x I think it is happening > >>>>>> because gcRMA is producing a lot of probes with identical > >>>>>> expression values. > >>>>>> > >>>>>> Here is a test session that causes the error. Upon request I can > >>>>>> provide a tarball of the test data but any collection of > >> CEL files > >>>>>> will reproduce the error. > >>>>>> The error also occurs if you run gcRMA from within > >> onecolorGUI or > >>>>>> affylmGUI. > >>>>>> It also happens if you first write the expression data to a file > >>>>>> with write.exprs, then read it back in with read.table. > >>>>>> > >>>>>> #Loading the packages > >>>>>>> library(affy) > >>>>>> Loading required package: Biobase > >>>>>> Loading required package: tools > >>>>>> > >>>>>>> library(gcrma) > >>>>>> Loading required package: matchprobes Loading required package: > >>>>>> splines > >>>>>> > >>>>>>> library(LPE) > >>>>>>> set.seed(0) > >>>>>> > >>>>>> #Reading in 4 CEL files > >>>>>>> test.Dat<-ReadAffy() > >>>>>> > >>>>>> #Summarizing with gcRMA > >>>>>>> test.gcrma<-gcrma(test.Dat) > >>>>>> Adjusting for non-specific binding....Done. > >>>>>> Normalizing > >>>>>> Calculating Expression > >>>>>> > >>>>>> #Summarizing with RMA > >>>>>>> test.rma<-rma(test.Dat) > >>>>>> Background correcting > >>>>>> Normalizing > >>>>>> Calculating Expression > >>>>>> > >>>>>> #Extracting gcRMA assay data > >>>>>>> test.gcrma.MAT<-exprs(test.gcrma) > >>>>>>> dim(test.gcrma.MAT) > >>>>>> [1] 15611 4 > >>>>>> > >>>>>> #Extracting RMA assay data > >>>>>> > >>>>>>> test.rma.MAT<-exprs(test.rma) > >>>>>>> dim(test.rma.MAT) > >>>>>> [1] 15611 4 > >>>>>> > >>>>>> #Running LPE function on gcRMA data and the resulting error > >>>>>>> var.test.gcrma<-baseOlig.error(test.gcrma.MAT, q= 0.01) > >>>>>> Error in var.M.adap[i] <- ifelse(!is.na(var.M.adap[i - 1]), > >>>>>> mean(var.M.adap[i + : > >>>>>> replacement has length zero > >>>>>> > >>>>>> #Running LPE function on RMA data - it successfully completes > >>>>>>> var.test.rma<-baseOlig.error(test.rma.MAT, q= 0.01) > >>>>>>> > >>>>>> > >>>>>> #My session info > >>>>>>> sessionInfo() > >>>>>> R version 2.8.0 (2008-10-20) > >>>>>> i386-apple-darwin8.11.1 > >>>>>> > >>>>>> locale: > >>>>>> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > >>>>>> > >>>>>> attached base packages: > >>>>>> [1] splines tools stats graphics grDevices utils > >>>>>> datasets methods base > >>>>>> > >>>>>> other attached packages: > >>>>>> [1] xenopuslaevisprobe_2.3.0 xenopuslaeviscdf_2.3.0 > >>>>>> LPE_1.16.0 gcrma_2.14.0 > >>>>>> matchprobes_1.14.0 affy_1.20.0 Biobase_2.2.0 > >>>>>> > >>>>>> loaded via a namespace (and not attached): > >>>>>> [1] affyio_1.10.0 preprocessCore_1.4.0 > >>>>>> > >>>>>> Thanks a lot for your help > >>>>>> > >>>>>> Charlie > >>>>>> > >>>>>> > >> ------------------------------------------------------------------- > >>>>>> --------- > >>>>>> > >>>>>> Charlie Whittaker, Ph.D. > >>>>>> Bioinformatics and Computing Core Facility The David H. Koch > >>>>>> Institute for Integrative Cancer Research At MIT > >>>>>> 77 Mass Ave E18-366 > >>>>>> Cambridge, MA 02139 > >>>>>> > >>>>>> 617-324-0337 > >>>>>> > >>> > >> > >> _______________________________________________ > >> Bioconductor mailing list > >> Bioconductor at stat.math.ethz.ch > >> https://stat.ethz.ch/mailman/listinfo/bioconductor > >> Search the archives: > >> http://news.gmane.org/gmane.science.biology.informatics.conductor > >> > >> > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLYlink written 10.8 years ago by laurent140
Thank you But the commands return "syntax error" What/how must I install to make this work? Thank you again > From: laurent <lgautier at="" gmail.com=""> > Date: Wed, 05 Nov 2008 08:25:20 +0100 > To: Loren Engrav <engrav at="" u.washington.edu=""> > Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch=""> > Subject: Re: [BioC] LPE error caused by gcRMA [Error invar.M.adap[i] <- > ifelse(!is.na(var.M.adap[i - 1]), mean(var.M.adap[i + : replacement has length > zero] > > > > On Tue, 2008-11-04 at 20:12 -0800, Loren Engrav wrote: >> I also did gcrma (and maanova) in 2006 and did not write down version >> numbers (stupid me), and now am processing the data >> >> Is there a page where version numbers of packages are listed by date? >> > > The VCS records all changes by date, and the file DESCRIPTION will > contain the package version number change. > > svn log gcrma/DESCRIPTION > > Look for the word 'release' or 'version' and note the revision numbers > you are interested in and: > > svn diff -r<revision number=""> gcrma/DESCRIPTION | grep Version > > > L. > >> >> >>> From: "Hooiveld, Guido" <guido.hooiveld at="" wur.nl=""> >>> Date: Tue, 4 Nov 2008 12:51:30 +0100 >>> To: charliew <charliew at="" mit.edu="">, Wolfgang Huber <huber at="" ebi.ac.uk=""> >>> Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch=""> >>> Subject: Re: [BioC] LPE error caused by gcRMA [Error invar.M.adap[i] <- >>> ifelse(!is.na(var.M.adap[i - 1]), mean(var.M.adap[i + : replacement has >>> length >>> zero] >>> >>> >>> Hi, >>> >>> Just to confirm that I and others also observed that since recently >>> GCRMA (>v 2.12) produces identical values for many probesets. >>> See e.g.: >>> http://thread.gmane.org/gmane.science.biology.informatics.conducto r/1884 >>> 4/focus=18914 >>> This behaviour is related to a modification in how Gene Specific >>> Background (GSB) is handled in GCRMA v2.12, compared to previous >>> versions. >>> >>> G >>> >>>> -----Original Message----- >>>> From: bioconductor-bounces at stat.math.ethz.ch >>>> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of charliew >>>> Sent: 04 November 2008 12:12 >>>> To: Wolfgang Huber >>>> Cc: bioconductor at stat.math.ethz.ch >>>> Subject: Re: [BioC] LPE error caused by gcRMA [Error >>>> invar.M.adap[i] <- ifelse(!is.na(var.M.adap[i - >>>> 1]),mean(var.M.adap[i + : replacement has length zero] >>>> >>>> Hi Wolfgang, >>>> >>>>> (i) do you (and others) consider this an "error", or rather "bad >>>>> behaviour" or "poor performance"? >>>> >>>> I'd have to say it is an error because I feel like it should >>>> work but it doesn't. Although it is also bad behaviour and >>>> poor performance. >>>> >>>>> (ii) and is it gcrma, or LPE that errs or poorly performs? >>>> >>>> I don't really know. Both packages can work fine. >>>> >>>> LPE works great for RMA data or any other data matrices from >>>> different array platforms. It just does not work on any gcRMA >>>> data that I have tried. >>>> >>>> gcRMA produces very reasonable summarized data so it seems to >>>> work fine too. >>>> >>>> things break down when I try to take gcRMA data to LPE. I >>>> feel like it has something to do with rows that have >>>> identical values in all lanes. >>>> I think that might be a newer "feature" of gcRMA but I'm not sure. >>>> >>>> The context of this question is I have a batch of old array >>>> data that is being prepped for publication. >>>> Back in early 2006 I identified a set of potentially >>>> differentially expressed genes by summarizing the data with >>>> gcRMA, then diff testing with LPE. >>>> >>>> Unfortunately I didn't note versions of software and whatnot. >>>> Totally my fault. >>>> >>>> To gather the information I needed to write a good methods >>>> section, I wanted to repeat the analysis right now and more >>>> carefully document what I did. >>>> Trouble is, I get this error out of LPE and that is making it >>>> hard to exactly duplicate the old results. >>>> >>>> One thing I know for sure is the old and new gcRMA data are >>>> not identical so that lead me to think that a gcRMA change is >>>> the source of the problem. >>>> >>>>> (iii) and are any of the maintainers of these packages >>>> interested in >>>>> these questions? >>>> >>>> hopefully... >>>> >>>>> Best wishes >>>>> Wolfgang >>>>> >>>>> ------------------------------------------------------------------ >>>>> Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber >>>>> >>>>> >>>>> 31/10/2008 20:05 charliew scripsit >>>>>> Hi Patrick, >>>>>> Thanks a lot for the quick reply. I updated the package >>>> and it didn't >>>>>> fix the error. >>>>>> >>>>>> c >>>>>> On Oct 31, 2008, at 3:29 PM, Patrick Aboyoun wrote: >>>>>> >>>>>>> Charlie, >>>>>>> I don't know if this is related to you issue, but a bug >>>> in the gcrma >>>>>>> package was just fixed and there is a version 2.14.1 is now up on >>>>>>> bioconductor.org. Update to the latest version of gcrma >>>> and see if >>>>>>> it addresses your issue. >>>>>>> >>>>>>> >>>>>>> Patrick >>>>>>> >>>>>>> >>>>>>> >>>>>>> charliew wrote: >>>>>>>> Dear List, >>>>>>>> I've encountered the following error when running LPE: >>>>>>>> >>>>>>>> Error in var.M.adap[i] <- ifelse(!is.na(var.M.adap[i - 1]), >>>>>>>> mean(var.M.adap[i + : >>>>>>>> replacement has length zero >>>>>>>> >>>>>>>> It happens when the CEL files have been processed with gcRMA but >>>>>>>> not when they have been processed with RMA. >>>>>>>> I'm not positive about this but I think this error first started >>>>>>>> happening with the upgrade to gcRMA 2.x I think it is happening >>>>>>>> because gcRMA is producing a lot of probes with identical >>>>>>>> expression values. >>>>>>>> >>>>>>>> Here is a test session that causes the error. Upon request I can >>>>>>>> provide a tarball of the test data but any collection of >>>> CEL files >>>>>>>> will reproduce the error. >>>>>>>> The error also occurs if you run gcRMA from within >>>> onecolorGUI or >>>>>>>> affylmGUI. >>>>>>>> It also happens if you first write the expression data to a file >>>>>>>> with write.exprs, then read it back in with read.table. >>>>>>>> >>>>>>>> #Loading the packages >>>>>>>>> library(affy) >>>>>>>> Loading required package: Biobase >>>>>>>> Loading required package: tools >>>>>>>> >>>>>>>>> library(gcrma) >>>>>>>> Loading required package: matchprobes Loading required package: >>>>>>>> splines >>>>>>>> >>>>>>>>> library(LPE) >>>>>>>>> set.seed(0) >>>>>>>> >>>>>>>> #Reading in 4 CEL files >>>>>>>>> test.Dat<-ReadAffy() >>>>>>>> >>>>>>>> #Summarizing with gcRMA >>>>>>>>> test.gcrma<-gcrma(test.Dat) >>>>>>>> Adjusting for non-specific binding....Done. >>>>>>>> Normalizing >>>>>>>> Calculating Expression >>>>>>>> >>>>>>>> #Summarizing with RMA >>>>>>>>> test.rma<-rma(test.Dat) >>>>>>>> Background correcting >>>>>>>> Normalizing >>>>>>>> Calculating Expression >>>>>>>> >>>>>>>> #Extracting gcRMA assay data >>>>>>>>> test.gcrma.MAT<-exprs(test.gcrma) >>>>>>>>> dim(test.gcrma.MAT) >>>>>>>> [1] 15611 4 >>>>>>>> >>>>>>>> #Extracting RMA assay data >>>>>>>> >>>>>>>>> test.rma.MAT<-exprs(test.rma) >>>>>>>>> dim(test.rma.MAT) >>>>>>>> [1] 15611 4 >>>>>>>> >>>>>>>> #Running LPE function on gcRMA data and the resulting error >>>>>>>>> var.test.gcrma<-baseOlig.error(test.gcrma.MAT, q= 0.01) >>>>>>>> Error in var.M.adap[i] <- ifelse(!is.na(var.M.adap[i - 1]), >>>>>>>> mean(var.M.adap[i + : >>>>>>>> replacement has length zero >>>>>>>> >>>>>>>> #Running LPE function on RMA data - it successfully completes >>>>>>>>> var.test.rma<-baseOlig.error(test.rma.MAT, q= 0.01) >>>>>>>>> >>>>>>>> >>>>>>>> #My session info >>>>>>>>> sessionInfo() >>>>>>>> R version 2.8.0 (2008-10-20) >>>>>>>> i386-apple-darwin8.11.1 >>>>>>>> >>>>>>>> locale: >>>>>>>> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 >>>>>>>> >>>>>>>> attached base packages: >>>>>>>> [1] splines tools stats graphics grDevices utils >>>>>>>> datasets methods base >>>>>>>> >>>>>>>> other attached packages: >>>>>>>> [1] xenopuslaevisprobe_2.3.0 xenopuslaeviscdf_2.3.0 >>>>>>>> LPE_1.16.0 gcrma_2.14.0 >>>>>>>> matchprobes_1.14.0 affy_1.20.0 Biobase_2.2.0 >>>>>>>> >>>>>>>> loaded via a namespace (and not attached): >>>>>>>> [1] affyio_1.10.0 preprocessCore_1.4.0 >>>>>>>> >>>>>>>> Thanks a lot for your help >>>>>>>> >>>>>>>> Charlie >>>>>>>> >>>>>>>> >>>> ------------------------------------------------------------------- >>>>>>>> --------- >>>>>>>> >>>>>>>> Charlie Whittaker, Ph.D. >>>>>>>> Bioinformatics and Computing Core Facility The David H. Koch >>>>>>>> Institute for Integrative Cancer Research At MIT >>>>>>>> 77 Mass Ave E18-366 >>>>>>>> Cambridge, MA 02139 >>>>>>>> >>>>>>>> 617-324-0337 >>>>>>>> >>>>> >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at stat.math.ethz.ch >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>>> >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD REPLYlink written 10.8 years ago by Loren Engrav1.0k
http://wiki.fhcrc.org/bioc/SvnHowTo (cygwin - or other providing 'grep' - probably needs to be installed if working w/ Microsoft Windows) L. On Thu, 2008-11-06 at 21:05 -0800, Loren Engrav wrote: > Thank you > But the commands return "syntax error" > What/how must I install to make this work? > Thank you again > > > > From: laurent <lgautier at="" gmail.com=""> > > Date: Wed, 05 Nov 2008 08:25:20 +0100 > > To: Loren Engrav <engrav at="" u.washington.edu=""> > > Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch=""> > > Subject: Re: [BioC] LPE error caused by gcRMA [Error invar.M.adap[i] <- > > ifelse(!is.na(var.M.adap[i - 1]), mean(var.M.adap[i + : replacement has length > > zero] > > > > > > > > On Tue, 2008-11-04 at 20:12 -0800, Loren Engrav wrote: > >> I also did gcrma (and maanova) in 2006 and did not write down version > >> numbers (stupid me), and now am processing the data > >> > >> Is there a page where version numbers of packages are listed by date? > >> > > > > The VCS records all changes by date, and the file DESCRIPTION will > > contain the package version number change. > > > > svn log gcrma/DESCRIPTION > > > > Look for the word 'release' or 'version' and note the revision numbers > > you are interested in and: > > > > svn diff -r<revision number=""> gcrma/DESCRIPTION | grep Version > > > > > > L. > > > >> > >> > >>> From: "Hooiveld, Guido" <guido.hooiveld at="" wur.nl=""> > >>> Date: Tue, 4 Nov 2008 12:51:30 +0100 > >>> To: charliew <charliew at="" mit.edu="">, Wolfgang Huber <huber at="" ebi.ac.uk=""> > >>> Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch=""> > >>> Subject: Re: [BioC] LPE error caused by gcRMA [Error invar.M.adap[i] <- > >>> ifelse(!is.na(var.M.adap[i - 1]), mean(var.M.adap[i + : replacement has > >>> length > >>> zero] > >>> > >>> > >>> Hi, > >>> > >>> Just to confirm that I and others also observed that since recently > >>> GCRMA (>v 2.12) produces identical values for many probesets. > >>> See e.g.: > >>> http://thread.gmane.org/gmane.science.biology.informatics.conduc tor/1884 > >>> 4/focus=18914 > >>> This behaviour is related to a modification in how Gene Specific > >>> Background (GSB) is handled in GCRMA v2.12, compared to previous > >>> versions. > >>> > >>> G > >>> > >>>> -----Original Message----- > >>>> From: bioconductor-bounces at stat.math.ethz.ch > >>>> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of charliew > >>>> Sent: 04 November 2008 12:12 > >>>> To: Wolfgang Huber > >>>> Cc: bioconductor at stat.math.ethz.ch > >>>> Subject: Re: [BioC] LPE error caused by gcRMA [Error > >>>> invar.M.adap[i] <- ifelse(!is.na(var.M.adap[i - > >>>> 1]),mean(var.M.adap[i + : replacement has length zero] > >>>> > >>>> Hi Wolfgang, > >>>> > >>>>> (i) do you (and others) consider this an "error", or rather "bad > >>>>> behaviour" or "poor performance"? > >>>> > >>>> I'd have to say it is an error because I feel like it should > >>>> work but it doesn't. Although it is also bad behaviour and > >>>> poor performance. > >>>> > >>>>> (ii) and is it gcrma, or LPE that errs or poorly performs? > >>>> > >>>> I don't really know. Both packages can work fine. > >>>> > >>>> LPE works great for RMA data or any other data matrices from > >>>> different array platforms. It just does not work on any gcRMA > >>>> data that I have tried. > >>>> > >>>> gcRMA produces very reasonable summarized data so it seems to > >>>> work fine too. > >>>> > >>>> things break down when I try to take gcRMA data to LPE. I > >>>> feel like it has something to do with rows that have > >>>> identical values in all lanes. > >>>> I think that might be a newer "feature" of gcRMA but I'm not sure. > >>>> > >>>> The context of this question is I have a batch of old array > >>>> data that is being prepped for publication. > >>>> Back in early 2006 I identified a set of potentially > >>>> differentially expressed genes by summarizing the data with > >>>> gcRMA, then diff testing with LPE. > >>>> > >>>> Unfortunately I didn't note versions of software and whatnot. > >>>> Totally my fault. > >>>> > >>>> To gather the information I needed to write a good methods > >>>> section, I wanted to repeat the analysis right now and more > >>>> carefully document what I did. > >>>> Trouble is, I get this error out of LPE and that is making it > >>>> hard to exactly duplicate the old results. > >>>> > >>>> One thing I know for sure is the old and new gcRMA data are > >>>> not identical so that lead me to think that a gcRMA change is > >>>> the source of the problem. > >>>> > >>>>> (iii) and are any of the maintainers of these packages > >>>> interested in > >>>>> these questions? > >>>> > >>>> hopefully... > >>>> > >>>>> Best wishes > >>>>> Wolfgang > >>>>> > >>>>> ------------------------------------------------------------------ > >>>>> Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber > >>>>> > >>>>> > >>>>> 31/10/2008 20:05 charliew scripsit > >>>>>> Hi Patrick, > >>>>>> Thanks a lot for the quick reply. I updated the package > >>>> and it didn't > >>>>>> fix the error. > >>>>>> > >>>>>> c > >>>>>> On Oct 31, 2008, at 3:29 PM, Patrick Aboyoun wrote: > >>>>>> > >>>>>>> Charlie, > >>>>>>> I don't know if this is related to you issue, but a bug > >>>> in the gcrma > >>>>>>> package was just fixed and there is a version 2.14.1 is now up on > >>>>>>> bioconductor.org. Update to the latest version of gcrma > >>>> and see if > >>>>>>> it addresses your issue. > >>>>>>> > >>>>>>> > >>>>>>> Patrick > >>>>>>> > >>>>>>> > >>>>>>> > >>>>>>> charliew wrote: > >>>>>>>> Dear List, > >>>>>>>> I've encountered the following error when running LPE: > >>>>>>>> > >>>>>>>> Error in var.M.adap[i] <- ifelse(!is.na(var.M.adap[i - 1]), > >>>>>>>> mean(var.M.adap[i + : > >>>>>>>> replacement has length zero > >>>>>>>> > >>>>>>>> It happens when the CEL files have been processed with gcRMA but > >>>>>>>> not when they have been processed with RMA. > >>>>>>>> I'm not positive about this but I think this error first started > >>>>>>>> happening with the upgrade to gcRMA 2.x I think it is happening > >>>>>>>> because gcRMA is producing a lot of probes with identical > >>>>>>>> expression values. > >>>>>>>> > >>>>>>>> Here is a test session that causes the error. Upon request I can > >>>>>>>> provide a tarball of the test data but any collection of > >>>> CEL files > >>>>>>>> will reproduce the error. > >>>>>>>> The error also occurs if you run gcRMA from within > >>>> onecolorGUI or > >>>>>>>> affylmGUI. > >>>>>>>> It also happens if you first write the expression data to a file > >>>>>>>> with write.exprs, then read it back in with read.table. > >>>>>>>> > >>>>>>>> #Loading the packages > >>>>>>>>> library(affy) > >>>>>>>> Loading required package: Biobase > >>>>>>>> Loading required package: tools > >>>>>>>> > >>>>>>>>> library(gcrma) > >>>>>>>> Loading required package: matchprobes Loading required package: > >>>>>>>> splines > >>>>>>>> > >>>>>>>>> library(LPE) > >>>>>>>>> set.seed(0) > >>>>>>>> > >>>>>>>> #Reading in 4 CEL files > >>>>>>>>> test.Dat<-ReadAffy() > >>>>>>>> > >>>>>>>> #Summarizing with gcRMA > >>>>>>>>> test.gcrma<-gcrma(test.Dat) > >>>>>>>> Adjusting for non-specific binding....Done. > >>>>>>>> Normalizing > >>>>>>>> Calculating Expression > >>>>>>>> > >>>>>>>> #Summarizing with RMA > >>>>>>>>> test.rma<-rma(test.Dat) > >>>>>>>> Background correcting > >>>>>>>> Normalizing > >>>>>>>> Calculating Expression > >>>>>>>> > >>>>>>>> #Extracting gcRMA assay data > >>>>>>>>> test.gcrma.MAT<-exprs(test.gcrma) > >>>>>>>>> dim(test.gcrma.MAT) > >>>>>>>> [1] 15611 4 > >>>>>>>> > >>>>>>>> #Extracting RMA assay data > >>>>>>>> > >>>>>>>>> test.rma.MAT<-exprs(test.rma) > >>>>>>>>> dim(test.rma.MAT) > >>>>>>>> [1] 15611 4 > >>>>>>>> > >>>>>>>> #Running LPE function on gcRMA data and the resulting error > >>>>>>>>> var.test.gcrma<-baseOlig.error(test.gcrma.MAT, q= 0.01) > >>>>>>>> Error in var.M.adap[i] <- ifelse(!is.na(var.M.adap[i - 1]), > >>>>>>>> mean(var.M.adap[i + : > >>>>>>>> replacement has length zero > >>>>>>>> > >>>>>>>> #Running LPE function on RMA data - it successfully completes > >>>>>>>>> var.test.rma<-baseOlig.error(test.rma.MAT, q= 0.01) > >>>>>>>>> > >>>>>>>> > >>>>>>>> #My session info > >>>>>>>>> sessionInfo() > >>>>>>>> R version 2.8.0 (2008-10-20) > >>>>>>>> i386-apple-darwin8.11.1 > >>>>>>>> > >>>>>>>> locale: > >>>>>>>> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > >>>>>>>> > >>>>>>>> attached base packages: > >>>>>>>> [1] splines tools stats graphics grDevices utils > >>>>>>>> datasets methods base > >>>>>>>> > >>>>>>>> other attached packages: > >>>>>>>> [1] xenopuslaevisprobe_2.3.0 xenopuslaeviscdf_2.3.0 > >>>>>>>> LPE_1.16.0 gcrma_2.14.0 > >>>>>>>> matchprobes_1.14.0 affy_1.20.0 Biobase_2.2.0 > >>>>>>>> > >>>>>>>> loaded via a namespace (and not attached): > >>>>>>>> [1] affyio_1.10.0 preprocessCore_1.4.0 > >>>>>>>> > >>>>>>>> Thanks a lot for your help > >>>>>>>> > >>>>>>>> Charlie > >>>>>>>> > >>>>>>>> > >>>> ------------------------------------------------------------------- > >>>>>>>> --------- > >>>>>>>> > >>>>>>>> Charlie Whittaker, Ph.D. > >>>>>>>> Bioinformatics and Computing Core Facility The David H. Koch > >>>>>>>> Institute for Integrative Cancer Research At MIT > >>>>>>>> 77 Mass Ave E18-366 > >>>>>>>> Cambridge, MA 02139 > >>>>>>>> > >>>>>>>> 617-324-0337 > >>>>>>>> > >>>>> > >>>> > >>>> _______________________________________________ > >>>> Bioconductor mailing list > >>>> Bioconductor at stat.math.ethz.ch > >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor > >>>> Search the archives: > >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor > >>>> > >>>> > >>> > >>> _______________________________________________ > >>> Bioconductor mailing list > >>> Bioconductor at stat.math.ethz.ch > >>> https://stat.ethz.ch/mailman/listinfo/bioconductor > >>> Search the archives: > >>> http://news.gmane.org/gmane.science.biology.informatics.conductor > >> > >> _______________________________________________ > >> Bioconductor mailing list > >> Bioconductor at stat.math.ethz.ch > >> https://stat.ethz.ch/mailman/listinfo/bioconductor > >> Search the archives: > >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLYlink written 10.8 years ago by laurent140
Ok thank you Am on MacOS 10.5.5 by the way So I went here for directions http://wiki.fhcrc.org/bioc/SvnHowTo And here to get Subversion http://subversion.tigris.org And installed it and set it up with sudo svnadmin create /usr/local/bin/repos And got the password from http://wiki.fhcrc.org/bioc/DeveloperPage And now have "svn log https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gcrma/DESC RIPTIO N" Working and see a long list of stuff including r5635 | dfcimm1 | 2003-09-15 14:16:39 -0700 (Mon, 15 Sep 2003) | 2 lines RI: version number change So I try "svn diff -r<r5635> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gcrma/DESC RIPTIO N | grep Version " And get -bash: r5635: No such file or directory Am I going to the wrong url? > From: laurent <lgautier at="" gmail.com=""> > Date: Fri, 07 Nov 2008 09:59:09 +0100 > To: Loren Engrav <engrav at="" u.washington.edu=""> > Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch=""> > Subject: Re: [BioC] LPE error caused by gcRMA [Error invar.M.adap[i] <- > ifelse(!is.na(var.M.adap[i - 1]), mean(var.M.adap[i + : replacement has length > zero] > > http://wiki.fhcrc.org/bioc/SvnHowTo > > (cygwin - or other providing 'grep' - probably needs to be installed if > working w/ Microsoft Windows) > > > L. > > > > > On Thu, 2008-11-06 at 21:05 -0800, Loren Engrav wrote: >> Thank you >> But the commands return "syntax error" >> What/how must I install to make this work? >> Thank you again >> >> >>> From: laurent <lgautier at="" gmail.com=""> >>> Date: Wed, 05 Nov 2008 08:25:20 +0100 >>> To: Loren Engrav <engrav at="" u.washington.edu=""> >>> Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch=""> >>> Subject: Re: [BioC] LPE error caused by gcRMA [Error invar.M.adap[i] <- >>> ifelse(!is.na(var.M.adap[i - 1]), mean(var.M.adap[i + : replacement has >>> length >>> zero] >>> >>> >>> >>> On Tue, 2008-11-04 at 20:12 -0800, Loren Engrav wrote: >>>> I also did gcrma (and maanova) in 2006 and did not write down version >>>> numbers (stupid me), and now am processing the data >>>> >>>> Is there a page where version numbers of packages are listed by date? >>>> >>> >>> The VCS records all changes by date, and the file DESCRIPTION will >>> contain the package version number change. >>> >>> svn log gcrma/DESCRIPTION >>> >>> Look for the word 'release' or 'version' and note the revision numbers >>> you are interested in and: >>> >>> svn diff -r<revision number=""> gcrma/DESCRIPTION | grep Version >>> >>> >>> L. >>> >>>> >>>> >>>>> From: "Hooiveld, Guido" <guido.hooiveld at="" wur.nl=""> >>>>> Date: Tue, 4 Nov 2008 12:51:30 +0100 >>>>> To: charliew <charliew at="" mit.edu="">, Wolfgang Huber <huber at="" ebi.ac.uk=""> >>>>> Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch=""> >>>>> Subject: Re: [BioC] LPE error caused by gcRMA [Error invar.M.adap[i] <- >>>>> ifelse(!is.na(var.M.adap[i - 1]), mean(var.M.adap[i + : replacement has >>>>> length >>>>> zero] >>>>> >>>>> >>>>> Hi, >>>>> >>>>> Just to confirm that I and others also observed that since recently >>>>> GCRMA (>v 2.12) produces identical values for many probesets. >>>>> See e.g.: >>>>> http://thread.gmane.org/gmane.science.biology.informatics.conduc tor/1884 >>>>> 4/focus=18914 >>>>> This behaviour is related to a modification in how Gene Specific >>>>> Background (GSB) is handled in GCRMA v2.12, compared to previous >>>>> versions. >>>>> >>>>> G >>>>> >>>>>> -----Original Message----- >>>>>> From: bioconductor-bounces at stat.math.ethz.ch >>>>>> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of charliew >>>>>> Sent: 04 November 2008 12:12 >>>>>> To: Wolfgang Huber >>>>>> Cc: bioconductor at stat.math.ethz.ch >>>>>> Subject: Re: [BioC] LPE error caused by gcRMA [Error >>>>>> invar.M.adap[i] <- ifelse(!is.na(var.M.adap[i - >>>>>> 1]),mean(var.M.adap[i + : replacement has length zero] >>>>>> >>>>>> Hi Wolfgang, >>>>>> >>>>>>> (i) do you (and others) consider this an "error", or rather "bad >>>>>>> behaviour" or "poor performance"? >>>>>> >>>>>> I'd have to say it is an error because I feel like it should >>>>>> work but it doesn't. Although it is also bad behaviour and >>>>>> poor performance. >>>>>> >>>>>>> (ii) and is it gcrma, or LPE that errs or poorly performs? >>>>>> >>>>>> I don't really know. Both packages can work fine. >>>>>> >>>>>> LPE works great for RMA data or any other data matrices from >>>>>> different array platforms. It just does not work on any gcRMA >>>>>> data that I have tried. >>>>>> >>>>>> gcRMA produces very reasonable summarized data so it seems to >>>>>> work fine too. >>>>>> >>>>>> things break down when I try to take gcRMA data to LPE. I >>>>>> feel like it has something to do with rows that have >>>>>> identical values in all lanes. >>>>>> I think that might be a newer "feature" of gcRMA but I'm not sure. >>>>>> >>>>>> The context of this question is I have a batch of old array >>>>>> data that is being prepped for publication. >>>>>> Back in early 2006 I identified a set of potentially >>>>>> differentially expressed genes by summarizing the data with >>>>>> gcRMA, then diff testing with LPE. >>>>>> >>>>>> Unfortunately I didn't note versions of software and whatnot. >>>>>> Totally my fault. >>>>>> >>>>>> To gather the information I needed to write a good methods >>>>>> section, I wanted to repeat the analysis right now and more >>>>>> carefully document what I did. >>>>>> Trouble is, I get this error out of LPE and that is making it >>>>>> hard to exactly duplicate the old results. >>>>>> >>>>>> One thing I know for sure is the old and new gcRMA data are >>>>>> not identical so that lead me to think that a gcRMA change is >>>>>> the source of the problem. >>>>>> >>>>>>> (iii) and are any of the maintainers of these packages >>>>>> interested in >>>>>>> these questions? >>>>>> >>>>>> hopefully... >>>>>> >>>>>>> Best wishes >>>>>>> Wolfgang >>>>>>> >>>>>>> ------------------------------------------------------------------ >>>>>>> Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber >>>>>>> >>>>>>> >>>>>>> 31/10/2008 20:05 charliew scripsit >>>>>>>> Hi Patrick, >>>>>>>> Thanks a lot for the quick reply. I updated the package >>>>>> and it didn't >>>>>>>> fix the error. >>>>>>>> >>>>>>>> c >>>>>>>> On Oct 31, 2008, at 3:29 PM, Patrick Aboyoun wrote: >>>>>>>> >>>>>>>>> Charlie, >>>>>>>>> I don't know if this is related to you issue, but a bug >>>>>> in the gcrma >>>>>>>>> package was just fixed and there is a version 2.14.1 is now up on >>>>>>>>> bioconductor.org. Update to the latest version of gcrma >>>>>> and see if >>>>>>>>> it addresses your issue. >>>>>>>>> >>>>>>>>> >>>>>>>>> Patrick >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> charliew wrote: >>>>>>>>>> Dear List, >>>>>>>>>> I've encountered the following error when running LPE: >>>>>>>>>> >>>>>>>>>> Error in var.M.adap[i] <- ifelse(!is.na(var.M.adap[i - 1]), >>>>>>>>>> mean(var.M.adap[i + : >>>>>>>>>> replacement has length zero >>>>>>>>>> >>>>>>>>>> It happens when the CEL files have been processed with gcRMA but >>>>>>>>>> not when they have been processed with RMA. >>>>>>>>>> I'm not positive about this but I think this error first started >>>>>>>>>> happening with the upgrade to gcRMA 2.x I think it is happening >>>>>>>>>> because gcRMA is producing a lot of probes with identical >>>>>>>>>> expression values. >>>>>>>>>> >>>>>>>>>> Here is a test session that causes the error. Upon request I can >>>>>>>>>> provide a tarball of the test data but any collection of >>>>>> CEL files >>>>>>>>>> will reproduce the error. >>>>>>>>>> The error also occurs if you run gcRMA from within >>>>>> onecolorGUI or >>>>>>>>>> affylmGUI. >>>>>>>>>> It also happens if you first write the expression data to a file >>>>>>>>>> with write.exprs, then read it back in with read.table. >>>>>>>>>> >>>>>>>>>> #Loading the packages >>>>>>>>>>> library(affy) >>>>>>>>>> Loading required package: Biobase >>>>>>>>>> Loading required package: tools >>>>>>>>>> >>>>>>>>>>> library(gcrma) >>>>>>>>>> Loading required package: matchprobes Loading required package: >>>>>>>>>> splines >>>>>>>>>> >>>>>>>>>>> library(LPE) >>>>>>>>>>> set.seed(0) >>>>>>>>>> >>>>>>>>>> #Reading in 4 CEL files >>>>>>>>>>> test.Dat<-ReadAffy() >>>>>>>>>> >>>>>>>>>> #Summarizing with gcRMA >>>>>>>>>>> test.gcrma<-gcrma(test.Dat) >>>>>>>>>> Adjusting for non-specific binding....Done. >>>>>>>>>> Normalizing >>>>>>>>>> Calculating Expression >>>>>>>>>> >>>>>>>>>> #Summarizing with RMA >>>>>>>>>>> test.rma<-rma(test.Dat) >>>>>>>>>> Background correcting >>>>>>>>>> Normalizing >>>>>>>>>> Calculating Expression >>>>>>>>>> >>>>>>>>>> #Extracting gcRMA assay data >>>>>>>>>>> test.gcrma.MAT<-exprs(test.gcrma) >>>>>>>>>>> dim(test.gcrma.MAT) >>>>>>>>>> [1] 15611 4 >>>>>>>>>> >>>>>>>>>> #Extracting RMA assay data >>>>>>>>>> >>>>>>>>>>> test.rma.MAT<-exprs(test.rma) >>>>>>>>>>> dim(test.rma.MAT) >>>>>>>>>> [1] 15611 4 >>>>>>>>>> >>>>>>>>>> #Running LPE function on gcRMA data and the resulting error >>>>>>>>>>> var.test.gcrma<-baseOlig.error(test.gcrma.MAT, q= 0.01) >>>>>>>>>> Error in var.M.adap[i] <- ifelse(!is.na(var.M.adap[i - 1]), >>>>>>>>>> mean(var.M.adap[i + : >>>>>>>>>> replacement has length zero >>>>>>>>>> >>>>>>>>>> #Running LPE function on RMA data - it successfully completes >>>>>>>>>>> var.test.rma<-baseOlig.error(test.rma.MAT, q= 0.01) >>>>>>>>>>> >>>>>>>>>> >>>>>>>>>> #My session info >>>>>>>>>>> sessionInfo() >>>>>>>>>> R version 2.8.0 (2008-10-20) >>>>>>>>>> i386-apple-darwin8.11.1 >>>>>>>>>> >>>>>>>>>> locale: >>>>>>>>>> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 >>>>>>>>>> >>>>>>>>>> attached base packages: >>>>>>>>>> [1] splines tools stats graphics grDevices utils >>>>>>>>>> datasets methods base >>>>>>>>>> >>>>>>>>>> other attached packages: >>>>>>>>>> [1] xenopuslaevisprobe_2.3.0 xenopuslaeviscdf_2.3.0 >>>>>>>>>> LPE_1.16.0 gcrma_2.14.0 >>>>>>>>>> matchprobes_1.14.0 affy_1.20.0 Biobase_2.2.0 >>>>>>>>>> >>>>>>>>>> loaded via a namespace (and not attached): >>>>>>>>>> [1] affyio_1.10.0 preprocessCore_1.4.0 >>>>>>>>>> >>>>>>>>>> Thanks a lot for your help >>>>>>>>>> >>>>>>>>>> Charlie >>>>>>>>>> >>>>>>>>>> >>>>>> ------------------------------------------------------------------- >>>>>>>>>> --------- >>>>>>>>>> >>>>>>>>>> Charlie Whittaker, Ph.D. >>>>>>>>>> Bioinformatics and Computing Core Facility The David H. Koch >>>>>>>>>> Institute for Integrative Cancer Research At MIT >>>>>>>>>> 77 Mass Ave E18-366 >>>>>>>>>> Cambridge, MA 02139 >>>>>>>>>> >>>>>>>>>> 617-324-0337 >>>>>>>>>> >>>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Bioconductor mailing list >>>>>> Bioconductor at stat.math.ethz.ch >>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>> Search the archives: >>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>>> >>>>>> >>>>> >>>>> _______________________________________________ >>>>> Bioconductor mailing list >>>>> Bioconductor at stat.math.ethz.ch >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>> Search the archives: >>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at stat.math.ethz.ch >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD REPLYlink written 10.8 years ago by Loren Engrav1.0k
On Mac OS X, subversion is included with the developer tools which you can either get from the Leopard DVD or you can sign up for an apple account (free) and download it from developer.apple.com. You probably want to do the last anyway, because it is nice to have the tools in their newest version. (tools = Xcode and friends) See below Kasper On Nov 7, 2008, at 12:13 , Loren Engrav wrote: > Ok thank you > Am on MacOS 10.5.5 by the way > > So I went here for directions > http://wiki.fhcrc.org/bioc/SvnHowTo > > And here to get Subversion > http://subversion.tigris.org > > And installed it and set it up with > sudo svnadmin create /usr/local/bin/repos I doubt this step is necessary > And got the password from > http://wiki.fhcrc.org/bioc/DeveloperPage > > And now have > "svn log > https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gcrma/DE SCRIPTIO > N" > Working and see a long list of stuff including > > r5635 | dfcimm1 | 2003-09-15 14:16:39 -0700 (Mon, 15 Sep 2003) | 2 > lines > RI: version number change > > So I try > "svn diff -r<r5635> > https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gcrma/DE SCRIPTIO > N | grep Version " > > And get > -bash: r5635: No such file or directory The syntax is -r5635 and not -r<5635> > Am I going to the wrong url? > > >> From: laurent <lgautier at="" gmail.com=""> >> Date: Fri, 07 Nov 2008 09:59:09 +0100 >> To: Loren Engrav <engrav at="" u.washington.edu=""> >> Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch=""> >> Subject: Re: [BioC] LPE error caused by gcRMA [Error >> invar.M.adap[i] <- >> ifelse(!is.na(var.M.adap[i - 1]), mean(var.M.adap[i + : replacement >> has length >> zero] >> >> http://wiki.fhcrc.org/bioc/SvnHowTo >> >> (cygwin - or other providing 'grep' - probably needs to be >> installed if >> working w/ Microsoft Windows) >> >> >> L. >> >> >> >> >> On Thu, 2008-11-06 at 21:05 -0800, Loren Engrav wrote: >>> Thank you >>> But the commands return "syntax error" >>> What/how must I install to make this work? >>> Thank you again >>> >>> >>>> From: laurent <lgautier at="" gmail.com=""> >>>> Date: Wed, 05 Nov 2008 08:25:20 +0100 >>>> To: Loren Engrav <engrav at="" u.washington.edu=""> >>>> Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch="">>>> > >>>> Subject: Re: [BioC] LPE error caused by gcRMA [Error >>>> invar.M.adap[i] <- >>>> ifelse(!is.na(var.M.adap[i - 1]), mean(var.M.adap[i + : >>>> replacement has >>>> length >>>> zero] >>>> >>>> >>>> >>>> On Tue, 2008-11-04 at 20:12 -0800, Loren Engrav wrote: >>>>> I also did gcrma (and maanova) in 2006 and did not write down >>>>> version >>>>> numbers (stupid me), and now am processing the data >>>>> >>>>> Is there a page where version numbers of packages are listed by >>>>> date? >>>>> >>>> >>>> The VCS records all changes by date, and the file DESCRIPTION will >>>> contain the package version number change. >>>> >>>> svn log gcrma/DESCRIPTION >>>> >>>> Look for the word 'release' or 'version' and note the revision >>>> numbers >>>> you are interested in and: >>>> >>>> svn diff -r<revision number=""> gcrma/DESCRIPTION | grep Version >>>> >>>> >>>> L. >>>> >>>>> >>>>> >>>>>> From: "Hooiveld, Guido" <guido.hooiveld at="" wur.nl=""> >>>>>> Date: Tue, 4 Nov 2008 12:51:30 +0100 >>>>>> To: charliew <charliew at="" mit.edu="">, Wolfgang Huber <huber at="" ebi.ac.uk=""> >>>>>> Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch="">>>>>> > >>>>>> Subject: Re: [BioC] LPE error caused by gcRMA [Error >>>>>> invar.M.adap[i] <- >>>>>> ifelse(!is.na(var.M.adap[i - 1]), mean(var.M.adap[i + : >>>>>> replacement has >>>>>> length >>>>>> zero] >>>>>> >>>>>> >>>>>> Hi, >>>>>> >>>>>> Just to confirm that I and others also observed that since >>>>>> recently >>>>>> GCRMA (>v 2.12) produces identical values for many probesets. >>>>>> See e.g.: >>>>>> http://thread.gmane.org/gmane.science.biology.informatics.condu ctor/1884 >>>>>> 4/focus=18914 >>>>>> This behaviour is related to a modification in how Gene Specific >>>>>> Background (GSB) is handled in GCRMA v2.12, compared to previous >>>>>> versions. >>>>>> >>>>>> G >>>>>> >>>>>>> -----Original Message----- >>>>>>> From: bioconductor-bounces at stat.math.ethz.ch >>>>>>> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of >>>>>>> charliew >>>>>>> Sent: 04 November 2008 12:12 >>>>>>> To: Wolfgang Huber >>>>>>> Cc: bioconductor at stat.math.ethz.ch >>>>>>> Subject: Re: [BioC] LPE error caused by gcRMA [Error >>>>>>> invar.M.adap[i] <- ifelse(!is.na(var.M.adap[i - >>>>>>> 1]),mean(var.M.adap[i + : replacement has length zero] >>>>>>> >>>>>>> Hi Wolfgang, >>>>>>> >>>>>>>> (i) do you (and others) consider this an "error", or rather >>>>>>>> "bad >>>>>>>> behaviour" or "poor performance"? >>>>>>> >>>>>>> I'd have to say it is an error because I feel like it should >>>>>>> work but it doesn't. Although it is also bad behaviour and >>>>>>> poor performance. >>>>>>> >>>>>>>> (ii) and is it gcrma, or LPE that errs or poorly performs? >>>>>>> >>>>>>> I don't really know. Both packages can work fine. >>>>>>> >>>>>>> LPE works great for RMA data or any other data matrices from >>>>>>> different array platforms. It just does not work on any gcRMA >>>>>>> data that I have tried. >>>>>>> >>>>>>> gcRMA produces very reasonable summarized data so it seems to >>>>>>> work fine too. >>>>>>> >>>>>>> things break down when I try to take gcRMA data to LPE. I >>>>>>> feel like it has something to do with rows that have >>>>>>> identical values in all lanes. >>>>>>> I think that might be a newer "feature" of gcRMA but I'm not >>>>>>> sure. >>>>>>> >>>>>>> The context of this question is I have a batch of old array >>>>>>> data that is being prepped for publication. >>>>>>> Back in early 2006 I identified a set of potentially >>>>>>> differentially expressed genes by summarizing the data with >>>>>>> gcRMA, then diff testing with LPE. >>>>>>> >>>>>>> Unfortunately I didn't note versions of software and whatnot. >>>>>>> Totally my fault. >>>>>>> >>>>>>> To gather the information I needed to write a good methods >>>>>>> section, I wanted to repeat the analysis right now and more >>>>>>> carefully document what I did. >>>>>>> Trouble is, I get this error out of LPE and that is making it >>>>>>> hard to exactly duplicate the old results. >>>>>>> >>>>>>> One thing I know for sure is the old and new gcRMA data are >>>>>>> not identical so that lead me to think that a gcRMA change is >>>>>>> the source of the problem. >>>>>>> >>>>>>>> (iii) and are any of the maintainers of these packages >>>>>>> interested in >>>>>>>> these questions? >>>>>>> >>>>>>> hopefully... >>>>>>> >>>>>>>> Best wishes >>>>>>>> Wolfgang >>>>>>>> >>>>>>>> ------------------------------------------------------------------ >>>>>>>> Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber >>>>>>>> >>>>>>>> >>>>>>>> 31/10/2008 20:05 charliew scripsit >>>>>>>>> Hi Patrick, >>>>>>>>> Thanks a lot for the quick reply. I updated the package >>>>>>> and it didn't >>>>>>>>> fix the error. >>>>>>>>> >>>>>>>>> c >>>>>>>>> On Oct 31, 2008, at 3:29 PM, Patrick Aboyoun wrote: >>>>>>>>> >>>>>>>>>> Charlie, >>>>>>>>>> I don't know if this is related to you issue, but a bug >>>>>>> in the gcrma >>>>>>>>>> package was just fixed and there is a version 2.14.1 is now >>>>>>>>>> up on >>>>>>>>>> bioconductor.org. Update to the latest version of gcrma >>>>>>> and see if >>>>>>>>>> it addresses your issue. >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Patrick >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> charliew wrote: >>>>>>>>>>> Dear List, >>>>>>>>>>> I've encountered the following error when running LPE: >>>>>>>>>>> >>>>>>>>>>> Error in var.M.adap[i] <- ifelse(!is.na(var.M.adap[i - 1]), >>>>>>>>>>> mean(var.M.adap[i + : >>>>>>>>>>> replacement has length zero >>>>>>>>>>> >>>>>>>>>>> It happens when the CEL files have been processed with >>>>>>>>>>> gcRMA but >>>>>>>>>>> not when they have been processed with RMA. >>>>>>>>>>> I'm not positive about this but I think this error first >>>>>>>>>>> started >>>>>>>>>>> happening with the upgrade to gcRMA 2.x I think it is >>>>>>>>>>> happening >>>>>>>>>>> because gcRMA is producing a lot of probes with identical >>>>>>>>>>> expression values. >>>>>>>>>>> >>>>>>>>>>> Here is a test session that causes the error. Upon request >>>>>>>>>>> I can >>>>>>>>>>> provide a tarball of the test data but any collection of >>>>>>> CEL files >>>>>>>>>>> will reproduce the error. >>>>>>>>>>> The error also occurs if you run gcRMA from within >>>>>>> onecolorGUI or >>>>>>>>>>> affylmGUI. >>>>>>>>>>> It also happens if you first write the expression data to >>>>>>>>>>> a file >>>>>>>>>>> with write.exprs, then read it back in with read.table. >>>>>>>>>>> >>>>>>>>>>> #Loading the packages >>>>>>>>>>>> library(affy) >>>>>>>>>>> Loading required package: Biobase >>>>>>>>>>> Loading required package: tools >>>>>>>>>>> >>>>>>>>>>>> library(gcrma) >>>>>>>>>>> Loading required package: matchprobes Loading required >>>>>>>>>>> package: >>>>>>>>>>> splines >>>>>>>>>>> >>>>>>>>>>>> library(LPE) >>>>>>>>>>>> set.seed(0) >>>>>>>>>>> >>>>>>>>>>> #Reading in 4 CEL files >>>>>>>>>>>> test.Dat<-ReadAffy() >>>>>>>>>>> >>>>>>>>>>> #Summarizing with gcRMA >>>>>>>>>>>> test.gcrma<-gcrma(test.Dat) >>>>>>>>>>> Adjusting for non-specific binding....Done. >>>>>>>>>>> Normalizing >>>>>>>>>>> Calculating Expression >>>>>>>>>>> >>>>>>>>>>> #Summarizing with RMA >>>>>>>>>>>> test.rma<-rma(test.Dat) >>>>>>>>>>> Background correcting >>>>>>>>>>> Normalizing >>>>>>>>>>> Calculating Expression >>>>>>>>>>> >>>>>>>>>>> #Extracting gcRMA assay data >>>>>>>>>>>> test.gcrma.MAT<-exprs(test.gcrma) >>>>>>>>>>>> dim(test.gcrma.MAT) >>>>>>>>>>> [1] 15611 4 >>>>>>>>>>> >>>>>>>>>>> #Extracting RMA assay data >>>>>>>>>>> >>>>>>>>>>>> test.rma.MAT<-exprs(test.rma) >>>>>>>>>>>> dim(test.rma.MAT) >>>>>>>>>>> [1] 15611 4 >>>>>>>>>>> >>>>>>>>>>> #Running LPE function on gcRMA data and the resulting error >>>>>>>>>>>> var.test.gcrma<-baseOlig.error(test.gcrma.MAT, q= 0.01) >>>>>>>>>>> Error in var.M.adap[i] <- ifelse(!is.na(var.M.adap[i - 1]), >>>>>>>>>>> mean(var.M.adap[i + : >>>>>>>>>>> replacement has length zero >>>>>>>>>>> >>>>>>>>>>> #Running LPE function on RMA data - it successfully >>>>>>>>>>> completes >>>>>>>>>>>> var.test.rma<-baseOlig.error(test.rma.MAT, q= 0.01) >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> #My session info >>>>>>>>>>>> sessionInfo() >>>>>>>>>>> R version 2.8.0 (2008-10-20) >>>>>>>>>>> i386-apple-darwin8.11.1 >>>>>>>>>>> >>>>>>>>>>> locale: >>>>>>>>>>> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 >>>>>>>>>>> >>>>>>>>>>> attached base packages: >>>>>>>>>>> [1] splines tools stats graphics grDevices utils >>>>>>>>>>> datasets methods base >>>>>>>>>>> >>>>>>>>>>> other attached packages: >>>>>>>>>>> [1] xenopuslaevisprobe_2.3.0 xenopuslaeviscdf_2.3.0 >>>>>>>>>>> LPE_1.16.0 gcrma_2.14.0 >>>>>>>>>>> matchprobes_1.14.0 affy_1.20.0 >>>>>>>>>>> Biobase_2.2.0 >>>>>>>>>>> >>>>>>>>>>> loaded via a namespace (and not attached): >>>>>>>>>>> [1] affyio_1.10.0 preprocessCore_1.4.0 >>>>>>>>>>> >>>>>>>>>>> Thanks a lot for your help >>>>>>>>>>> >>>>>>>>>>> Charlie >>>>>>>>>>> >>>>>>>>>>> >>>>>>> ------------------------------------------------------------------- >>>>>>>>>>> --------- >>>>>>>>>>> >>>>>>>>>>> Charlie Whittaker, Ph.D. >>>>>>>>>>> Bioinformatics and Computing Core Facility The David H. Koch >>>>>>>>>>> Institute for Integrative Cancer Research At MIT >>>>>>>>>>> 77 Mass Ave E18-366 >>>>>>>>>>> Cambridge, MA 02139 >>>>>>>>>>> >>>>>>>>>>> 617-324-0337 >>>>>>>>>>> >>>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Bioconductor mailing list >>>>>>> Bioconductor at stat.math.ethz.ch >>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>>> Search the archives: >>>>>>> http://news.gmane.org/ >>>>>>> gmane.science.biology.informatics.conductor >>>>>>> >>>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Bioconductor mailing list >>>>>> Bioconductor at stat.math.ethz.ch >>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>> Search the archives: >>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>> >>>>> _______________________________________________ >>>>> Bioconductor mailing list >>>>> Bioconductor at stat.math.ethz.ch >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>> Search the archives: >>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLYlink written 10.8 years ago by Kasper Daniel Hansen6.4k
Again, you are correct, and helpful Thank you > From: Kasper Daniel Hansen <khansen at="" stat.berkeley.edu=""> > Date: Fri, 7 Nov 2008 20:02:06 -0800 > To: Loren Engrav <engrav at="" u.washington.edu=""> > Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch=""> > Subject: Re: [BioC] LPE error caused by gcRMA [Error invar.M.adap[i] <- > ifelse(!is.na(var.M.adap[i - 1]), mean(var.M.adap[i + : replacement has length > zero] > > On Mac OS X, subversion is included with the developer tools which you > can either get from the Leopard DVD or you can sign up for an apple > account (free) and download it from developer.apple.com. You probably > want to do the last anyway, because it is nice to have the tools in > their newest version. (tools = Xcode and friends) > > See below > > Kasper > > On Nov 7, 2008, at 12:13 , Loren Engrav wrote: > >> Ok thank you >> Am on MacOS 10.5.5 by the way >> >> So I went here for directions >> http://wiki.fhcrc.org/bioc/SvnHowTo >> >> And here to get Subversion >> http://subversion.tigris.org >> >> And installed it and set it up with >> sudo svnadmin create /usr/local/bin/repos > > I doubt this step is necessary > >> And got the password from >> http://wiki.fhcrc.org/bioc/DeveloperPage >> >> And now have >> "svn log >> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gcrma/D ESCRIPTIO >> N" >> Working and see a long list of stuff including >> >> r5635 | dfcimm1 | 2003-09-15 14:16:39 -0700 (Mon, 15 Sep 2003) | 2 >> lines >> RI: version number change >> >> So I try >> "svn diff -r<r5635> >> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gcrma/D ESCRIPTIO >> N | grep Version " >> >> And get >> -bash: r5635: No such file or directory > > The syntax is -r5635 and not -r<5635> > > >> Am I going to the wrong url? >> >> >>> From: laurent <lgautier at="" gmail.com=""> >>> Date: Fri, 07 Nov 2008 09:59:09 +0100 >>> To: Loren Engrav <engrav at="" u.washington.edu=""> >>> Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch=""> >>> Subject: Re: [BioC] LPE error caused by gcRMA [Error >>> invar.M.adap[i] <- >>> ifelse(!is.na(var.M.adap[i - 1]), mean(var.M.adap[i + : replacement >>> has length >>> zero] >>> >>> http://wiki.fhcrc.org/bioc/SvnHowTo >>> >>> (cygwin - or other providing 'grep' - probably needs to be >>> installed if >>> working w/ Microsoft Windows) >>> >>> >>> L. >>> >>> >>> >>> >>> On Thu, 2008-11-06 at 21:05 -0800, Loren Engrav wrote: >>>> Thank you >>>> But the commands return "syntax error" >>>> What/how must I install to make this work? >>>> Thank you again >>>> >>>> >>>>> From: laurent <lgautier at="" gmail.com=""> >>>>> Date: Wed, 05 Nov 2008 08:25:20 +0100 >>>>> To: Loren Engrav <engrav at="" u.washington.edu=""> >>>>> Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch="">>>>>> >>>>> Subject: Re: [BioC] LPE error caused by gcRMA [Error >>>>> invar.M.adap[i] <- >>>>> ifelse(!is.na(var.M.adap[i - 1]), mean(var.M.adap[i + : >>>>> replacement has >>>>> length >>>>> zero] >>>>> >>>>> >>>>> >>>>> On Tue, 2008-11-04 at 20:12 -0800, Loren Engrav wrote: >>>>>> I also did gcrma (and maanova) in 2006 and did not write down >>>>>> version >>>>>> numbers (stupid me), and now am processing the data >>>>>> >>>>>> Is there a page where version numbers of packages are listed by >>>>>> date? >>>>>> >>>>> >>>>> The VCS records all changes by date, and the file DESCRIPTION will >>>>> contain the package version number change. >>>>> >>>>> svn log gcrma/DESCRIPTION >>>>> >>>>> Look for the word 'release' or 'version' and note the revision >>>>> numbers >>>>> you are interested in and: >>>>> >>>>> svn diff -r<revision number=""> gcrma/DESCRIPTION | grep Version >>>>> >>>>> >>>>> L. >>>>> >>>>>> >>>>>> >>>>>>> From: "Hooiveld, Guido" <guido.hooiveld at="" wur.nl=""> >>>>>>> Date: Tue, 4 Nov 2008 12:51:30 +0100 >>>>>>> To: charliew <charliew at="" mit.edu="">, Wolfgang Huber <huber at="" ebi.ac.uk=""> >>>>>>> Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch="">>>>>>>> >>>>>>> Subject: Re: [BioC] LPE error caused by gcRMA [Error >>>>>>> invar.M.adap[i] <- >>>>>>> ifelse(!is.na(var.M.adap[i - 1]), mean(var.M.adap[i + : >>>>>>> replacement has >>>>>>> length >>>>>>> zero] >>>>>>> >>>>>>> >>>>>>> Hi, >>>>>>> >>>>>>> Just to confirm that I and others also observed that since >>>>>>> recently >>>>>>> GCRMA (>v 2.12) produces identical values for many probesets. >>>>>>> See e.g.: >>>>>>> http://thread.gmane.org/gmane.science.biology.informatics.cond uctor/1884 >>>>>>> 4/focus=18914 >>>>>>> This behaviour is related to a modification in how Gene Specific >>>>>>> Background (GSB) is handled in GCRMA v2.12, compared to previous >>>>>>> versions. >>>>>>> >>>>>>> G >>>>>>> >>>>>>>> -----Original Message----- >>>>>>>> From: bioconductor-bounces at stat.math.ethz.ch >>>>>>>> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of >>>>>>>> charliew >>>>>>>> Sent: 04 November 2008 12:12 >>>>>>>> To: Wolfgang Huber >>>>>>>> Cc: bioconductor at stat.math.ethz.ch >>>>>>>> Subject: Re: [BioC] LPE error caused by gcRMA [Error >>>>>>>> invar.M.adap[i] <- ifelse(!is.na(var.M.adap[i - >>>>>>>> 1]),mean(var.M.adap[i + : replacement has length zero] >>>>>>>> >>>>>>>> Hi Wolfgang, >>>>>>>> >>>>>>>>> (i) do you (and others) consider this an "error", or rather >>>>>>>>> "bad >>>>>>>>> behaviour" or "poor performance"? >>>>>>>> >>>>>>>> I'd have to say it is an error because I feel like it should >>>>>>>> work but it doesn't. Although it is also bad behaviour and >>>>>>>> poor performance. >>>>>>>> >>>>>>>>> (ii) and is it gcrma, or LPE that errs or poorly performs? >>>>>>>> >>>>>>>> I don't really know. Both packages can work fine. >>>>>>>> >>>>>>>> LPE works great for RMA data or any other data matrices from >>>>>>>> different array platforms. It just does not work on any gcRMA >>>>>>>> data that I have tried. >>>>>>>> >>>>>>>> gcRMA produces very reasonable summarized data so it seems to >>>>>>>> work fine too. >>>>>>>> >>>>>>>> things break down when I try to take gcRMA data to LPE. I >>>>>>>> feel like it has something to do with rows that have >>>>>>>> identical values in all lanes. >>>>>>>> I think that might be a newer "feature" of gcRMA but I'm not >>>>>>>> sure. >>>>>>>> >>>>>>>> The context of this question is I have a batch of old array >>>>>>>> data that is being prepped for publication. >>>>>>>> Back in early 2006 I identified a set of potentially >>>>>>>> differentially expressed genes by summarizing the data with >>>>>>>> gcRMA, then diff testing with LPE. >>>>>>>> >>>>>>>> Unfortunately I didn't note versions of software and whatnot. >>>>>>>> Totally my fault. >>>>>>>> >>>>>>>> To gather the information I needed to write a good methods >>>>>>>> section, I wanted to repeat the analysis right now and more >>>>>>>> carefully document what I did. >>>>>>>> Trouble is, I get this error out of LPE and that is making it >>>>>>>> hard to exactly duplicate the old results. >>>>>>>> >>>>>>>> One thing I know for sure is the old and new gcRMA data are >>>>>>>> not identical so that lead me to think that a gcRMA change is >>>>>>>> the source of the problem. >>>>>>>> >>>>>>>>> (iii) and are any of the maintainers of these packages >>>>>>>> interested in >>>>>>>>> these questions? >>>>>>>> >>>>>>>> hopefully... >>>>>>>> >>>>>>>>> Best wishes >>>>>>>>> Wolfgang >>>>>>>>> >>>>>>>>> ------------------------------------------------------------------ >>>>>>>>> Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber >>>>>>>>> >>>>>>>>> >>>>>>>>> 31/10/2008 20:05 charliew scripsit >>>>>>>>>> Hi Patrick, >>>>>>>>>> Thanks a lot for the quick reply. I updated the package >>>>>>>> and it didn't >>>>>>>>>> fix the error. >>>>>>>>>> >>>>>>>>>> c >>>>>>>>>> On Oct 31, 2008, at 3:29 PM, Patrick Aboyoun wrote: >>>>>>>>>> >>>>>>>>>>> Charlie, >>>>>>>>>>> I don't know if this is related to you issue, but a bug >>>>>>>> in the gcrma >>>>>>>>>>> package was just fixed and there is a version 2.14.1 is now >>>>>>>>>>> up on >>>>>>>>>>> bioconductor.org. Update to the latest version of gcrma >>>>>>>> and see if >>>>>>>>>>> it addresses your issue. >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> Patrick >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> charliew wrote: >>>>>>>>>>>> Dear List, >>>>>>>>>>>> I've encountered the following error when running LPE: >>>>>>>>>>>> >>>>>>>>>>>> Error in var.M.adap[i] <- ifelse(!is.na(var.M.adap[i - 1]), >>>>>>>>>>>> mean(var.M.adap[i + : >>>>>>>>>>>> replacement has length zero >>>>>>>>>>>> >>>>>>>>>>>> It happens when the CEL files have been processed with >>>>>>>>>>>> gcRMA but >>>>>>>>>>>> not when they have been processed with RMA. >>>>>>>>>>>> I'm not positive about this but I think this error first >>>>>>>>>>>> started >>>>>>>>>>>> happening with the upgrade to gcRMA 2.x I think it is >>>>>>>>>>>> happening >>>>>>>>>>>> because gcRMA is producing a lot of probes with identical >>>>>>>>>>>> expression values. >>>>>>>>>>>> >>>>>>>>>>>> Here is a test session that causes the error. Upon request >>>>>>>>>>>> I can >>>>>>>>>>>> provide a tarball of the test data but any collection of >>>>>>>> CEL files >>>>>>>>>>>> will reproduce the error. >>>>>>>>>>>> The error also occurs if you run gcRMA from within >>>>>>>> onecolorGUI or >>>>>>>>>>>> affylmGUI. >>>>>>>>>>>> It also happens if you first write the expression data to >>>>>>>>>>>> a file >>>>>>>>>>>> with write.exprs, then read it back in with read.table. >>>>>>>>>>>> >>>>>>>>>>>> #Loading the packages >>>>>>>>>>>> library(affy) >>>>>>>>>>>> Loading required package: Biobase >>>>>>>>>>>> Loading required package: tools >>>>>>>>>>>> >>>>>>>>>>>> library(gcrma) >>>>>>>>>>>> Loading required package: matchprobes Loading required >>>>>>>>>>>> package: >>>>>>>>>>>> splines >>>>>>>>>>>> >>>>>>>>>>>> library(LPE) >>>>>>>>>>>> set.seed(0) >>>>>>>>>>>> >>>>>>>>>>>> #Reading in 4 CEL files >>>>>>>>>>>> test.Dat<-ReadAffy() >>>>>>>>>>>> >>>>>>>>>>>> #Summarizing with gcRMA >>>>>>>>>>>> test.gcrma<-gcrma(test.Dat) >>>>>>>>>>>> Adjusting for non-specific binding....Done. >>>>>>>>>>>> Normalizing >>>>>>>>>>>> Calculating Expression >>>>>>>>>>>> >>>>>>>>>>>> #Summarizing with RMA >>>>>>>>>>>> test.rma<-rma(test.Dat) >>>>>>>>>>>> Background correcting >>>>>>>>>>>> Normalizing >>>>>>>>>>>> Calculating Expression >>>>>>>>>>>> >>>>>>>>>>>> #Extracting gcRMA assay data >>>>>>>>>>>> test.gcrma.MAT<-exprs(test.gcrma) >>>>>>>>>>>> dim(test.gcrma.MAT) >>>>>>>>>>>> [1] 15611 4 >>>>>>>>>>>> >>>>>>>>>>>> #Extracting RMA assay data >>>>>>>>>>>> >>>>>>>>>>>> test.rma.MAT<-exprs(test.rma) >>>>>>>>>>>> dim(test.rma.MAT) >>>>>>>>>>>> [1] 15611 4 >>>>>>>>>>>> >>>>>>>>>>>> #Running LPE function on gcRMA data and the resulting error >>>>>>>>>>>> var.test.gcrma<-baseOlig.error(test.gcrma.MAT, q= 0.01) >>>>>>>>>>>> Error in var.M.adap[i] <- ifelse(!is.na(var.M.adap[i - 1]), >>>>>>>>>>>> mean(var.M.adap[i + : >>>>>>>>>>>> replacement has length zero >>>>>>>>>>>> >>>>>>>>>>>> #Running LPE function on RMA data - it successfully >>>>>>>>>>>> completes >>>>>>>>>>>> var.test.rma<-baseOlig.error(test.rma.MAT, q= 0.01) >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> #My session info >>>>>>>>>>>> sessionInfo() >>>>>>>>>>>> R version 2.8.0 (2008-10-20) >>>>>>>>>>>> i386-apple-darwin8.11.1 >>>>>>>>>>>> >>>>>>>>>>>> locale: >>>>>>>>>>>> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 >>>>>>>>>>>> >>>>>>>>>>>> attached base packages: >>>>>>>>>>>> [1] splines tools stats graphics grDevices utils >>>>>>>>>>>> datasets methods base >>>>>>>>>>>> >>>>>>>>>>>> other attached packages: >>>>>>>>>>>> [1] xenopuslaevisprobe_2.3.0 xenopuslaeviscdf_2.3.0 >>>>>>>>>>>> LPE_1.16.0 gcrma_2.14.0 >>>>>>>>>>>> matchprobes_1.14.0 affy_1.20.0 >>>>>>>>>>>> Biobase_2.2.0 >>>>>>>>>>>> >>>>>>>>>>>> loaded via a namespace (and not attached): >>>>>>>>>>>> [1] affyio_1.10.0 preprocessCore_1.4.0 >>>>>>>>>>>> >>>>>>>>>>>> Thanks a lot for your help >>>>>>>>>>>> >>>>>>>>>>>> Charlie >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>> ------------------------------------------------------------------- >>>>>>>>>>>> --------- >>>>>>>>>>>> >>>>>>>>>>>> Charlie Whittaker, Ph.D. >>>>>>>>>>>> Bioinformatics and Computing Core Facility The David H. Koch >>>>>>>>>>>> Institute for Integrative Cancer Research At MIT >>>>>>>>>>>> 77 Mass Ave E18-366 >>>>>>>>>>>> Cambridge, MA 02139 >>>>>>>>>>>> >>>>>>>>>>>> 617-324-0337 >>>>>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Bioconductor mailing list >>>>>>>> Bioconductor at stat.math.ethz.ch >>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>>>> Search the archives: >>>>>>>> http://news.gmane.org/ >>>>>>>> gmane.science.biology.informatics.conductor >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Bioconductor mailing list >>>>>>> Bioconductor at stat.math.ethz.ch >>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>>> Search the archives: >>>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>>> >>>>>> _______________________________________________ >>>>>> Bioconductor mailing list >>>>>> Bioconductor at stat.math.ethz.ch >>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>> Search the archives: >>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>> >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at stat.math.ethz.ch >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD REPLYlink written 10.8 years ago by Loren Engrav1.0k
So now trying svn diff -r xxxx https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gcrma/DESC RIPTIO N | grep Version And all seems work Thank you Ok thank you Am on MacOS 10.5.5 by the way So I went here for directions http://wiki.fhcrc.org/bioc/SvnHowTo And here to get Subversion http://subversion.tigris.org And installed it and set it up with sudo svnadmin create /usr/local/bin/repos And got the password from http://wiki.fhcrc.org/bioc/DeveloperPage And now have "svn log https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gcrma/DESC RIPTIO N" Working and see a long list of stuff including r5635 | dfcimm1 | 2003-09-15 14:16:39 -0700 (Mon, 15 Sep 2003) | 2 lines RI: version number change So I try "svn diff -r<r5635> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gcrma/DESC RIPTIO N | grep Version " And get -bash: r5635: No such file or directory Am I going to the wrong url? > From: laurent <lgautier at="" gmail.com=""> > Date: Fri, 07 Nov 2008 09:59:09 +0100 > To: Loren Engrav <engrav at="" u.washington.edu=""> > Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch=""> > Subject: Re: [BioC] LPE error caused by gcRMA [Error invar.M.adap[i] <- > ifelse(!is.na(var.M.adap[i - 1]), mean(var.M.adap[i + : replacement has length > zero] > > http://wiki.fhcrc.org/bioc/SvnHowTo > > (cygwin - or other providing 'grep' - probably needs to be installed if > working w/ Microsoft Windows) > > > L. > > > > > On Thu, 2008-11-06 at 21:05 -0800, Loren Engrav wrote: >> Thank you >> But the commands return "syntax error" >> What/how must I install to make this work? >> Thank you again >> >> >>> From: laurent <lgautier at="" gmail.com=""> >>> Date: Wed, 05 Nov 2008 08:25:20 +0100 >>> To: Loren Engrav <engrav at="" u.washington.edu=""> >>> Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch=""> >>> Subject: Re: [BioC] LPE error caused by gcRMA [Error invar.M.adap[i] <- >>> ifelse(!is.na(var.M.adap[i - 1]), mean(var.M.adap[i + : replacement has >>> length >>> zero] >>> >>> >>> >>> On Tue, 2008-11-04 at 20:12 -0800, Loren Engrav wrote: >>>> I also did gcrma (and maanova) in 2006 and did not write down version >>>> numbers (stupid me), and now am processing the data >>>> >>>> Is there a page where version numbers of packages are listed by date? >>>> >>> >>> The VCS records all changes by date, and the file DESCRIPTION will >>> contain the package version number change. >>> >>> svn log gcrma/DESCRIPTION >>> >>> Look for the word 'release' or 'version' and note the revision numbers >>> you are interested in and: >>> >>> svn diff -r<revision number=""> gcrma/DESCRIPTION | grep Version >>> >>> >>> L. >>> >>>> >>>> >>>>> From: "Hooiveld, Guido" <guido.hooiveld at="" wur.nl=""> >>>>> Date: Tue, 4 Nov 2008 12:51:30 +0100 >>>>> To: charliew <charliew at="" mit.edu="">, Wolfgang Huber <huber at="" ebi.ac.uk=""> >>>>> Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch=""> >>>>> Subject: Re: [BioC] LPE error caused by gcRMA [Error invar.M.adap[i] <- >>>>> ifelse(!is.na(var.M.adap[i - 1]), mean(var.M.adap[i + : replacement has >>>>> length >>>>> zero] >>>>> >>>>> >>>>> Hi, >>>>> >>>>> Just to confirm that I and others also observed that since recently >>>>> GCRMA (>v 2.12) produces identical values for many probesets. >>>>> See e.g.: >>>>> http://thread.gmane.org/gmane.science.biology.informatics.conduc tor/1884 >>>>> 4/focus=18914 >>>>> This behaviour is related to a modification in how Gene Specific >>>>> Background (GSB) is handled in GCRMA v2.12, compared to previous >>>>> versions. >>>>> >>>>> G >>>>> >>>>>> -----Original Message----- >>>>>> From: bioconductor-bounces at stat.math.ethz.ch >>>>>> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of charliew >>>>>> Sent: 04 November 2008 12:12 >>>>>> To: Wolfgang Huber >>>>>> Cc: bioconductor at stat.math.ethz.ch >>>>>> Subject: Re: [BioC] LPE error caused by gcRMA [Error >>>>>> invar.M.adap[i] <- ifelse(!is.na(var.M.adap[i - >>>>>> 1]),mean(var.M.adap[i + : replacement has length zero] >>>>>> >>>>>> Hi Wolfgang, >>>>>> >>>>>>> (i) do you (and others) consider this an "error", or rather "bad >>>>>>> behaviour" or "poor performance"? >>>>>> >>>>>> I'd have to say it is an error because I feel like it should >>>>>> work but it doesn't. Although it is also bad behaviour and >>>>>> poor performance. >>>>>> >>>>>>> (ii) and is it gcrma, or LPE that errs or poorly performs? >>>>>> >>>>>> I don't really know. Both packages can work fine. >>>>>> >>>>>> LPE works great for RMA data or any other data matrices from >>>>>> different array platforms. It just does not work on any gcRMA >>>>>> data that I have tried. >>>>>> >>>>>> gcRMA produces very reasonable summarized data so it seems to >>>>>> work fine too. >>>>>> >>>>>> things break down when I try to take gcRMA data to LPE. I >>>>>> feel like it has something to do with rows that have >>>>>> identical values in all lanes. >>>>>> I think that might be a newer "feature" of gcRMA but I'm not sure. >>>>>> >>>>>> The context of this question is I have a batch of old array >>>>>> data that is being prepped for publication. >>>>>> Back in early 2006 I identified a set of potentially >>>>>> differentially expressed genes by summarizing the data with >>>>>> gcRMA, then diff testing with LPE. >>>>>> >>>>>> Unfortunately I didn't note versions of software and whatnot. >>>>>> Totally my fault. >>>>>> >>>>>> To gather the information I needed to write a good methods >>>>>> section, I wanted to repeat the analysis right now and more >>>>>> carefully document what I did. >>>>>> Trouble is, I get this error out of LPE and that is making it >>>>>> hard to exactly duplicate the old results. >>>>>> >>>>>> One thing I know for sure is the old and new gcRMA data are >>>>>> not identical so that lead me to think that a gcRMA change is >>>>>> the source of the problem. >>>>>> >>>>>>> (iii) and are any of the maintainers of these packages >>>>>> interested in >>>>>>> these questions? >>>>>> >>>>>> hopefully... >>>>>> >>>>>>> Best wishes >>>>>>> Wolfgang >>>>>>> >>>>>>> ------------------------------------------------------------------ >>>>>>> Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber >>>>>>> >>>>>>> >>>>>>> 31/10/2008 20:05 charliew scripsit >>>>>>>> Hi Patrick, >>>>>>>> Thanks a lot for the quick reply. I updated the package >>>>>> and it didn't >>>>>>>> fix the error. >>>>>>>> >>>>>>>> c >>>>>>>> On Oct 31, 2008, at 3:29 PM, Patrick Aboyoun wrote: >>>>>>>> >>>>>>>>> Charlie, >>>>>>>>> I don't know if this is related to you issue, but a bug >>>>>> in the gcrma >>>>>>>>> package was just fixed and there is a version 2.14.1 is now up on >>>>>>>>> bioconductor.org. Update to the latest version of gcrma >>>>>> and see if >>>>>>>>> it addresses your issue. >>>>>>>>> >>>>>>>>> >>>>>>>>> Patrick >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> charliew wrote: >>>>>>>>>> Dear List, >>>>>>>>>> I've encountered the following error when running LPE: >>>>>>>>>> >>>>>>>>>> Error in var.M.adap[i] <- ifelse(!is.na(var.M.adap[i - 1]), >>>>>>>>>> mean(var.M.adap[i + : >>>>>>>>>> replacement has length zero >>>>>>>>>> >>>>>>>>>> It happens when the CEL files have been processed with gcRMA but >>>>>>>>>> not when they have been processed with RMA. >>>>>>>>>> I'm not positive about this but I think this error first started >>>>>>>>>> happening with the upgrade to gcRMA 2.x I think it is happening >>>>>>>>>> because gcRMA is producing a lot of probes with identical >>>>>>>>>> expression values. >>>>>>>>>> >>>>>>>>>> Here is a test session that causes the error. Upon request I can >>>>>>>>>> provide a tarball of the test data but any collection of >>>>>> CEL files >>>>>>>>>> will reproduce the error. >>>>>>>>>> The error also occurs if you run gcRMA from within >>>>>> onecolorGUI or >>>>>>>>>> affylmGUI. >>>>>>>>>> It also happens if you first write the expression data to a file >>>>>>>>>> with write.exprs, then read it back in with read.table. >>>>>>>>>> >>>>>>>>>> #Loading the packages >>>>>>>>>>> library(affy) >>>>>>>>>> Loading required package: Biobase >>>>>>>>>> Loading required package: tools >>>>>>>>>> >>>>>>>>>>> library(gcrma) >>>>>>>>>> Loading required package: matchprobes Loading required package: >>>>>>>>>> splines >>>>>>>>>> >>>>>>>>>>> library(LPE) >>>>>>>>>>> set.seed(0) >>>>>>>>>> >>>>>>>>>> #Reading in 4 CEL files >>>>>>>>>>> test.Dat<-ReadAffy() >>>>>>>>>> >>>>>>>>>> #Summarizing with gcRMA >>>>>>>>>>> test.gcrma<-gcrma(test.Dat) >>>>>>>>>> Adjusting for non-specific binding....Done. >>>>>>>>>> Normalizing >>>>>>>>>> Calculating Expression >>>>>>>>>> >>>>>>>>>> #Summarizing with RMA >>>>>>>>>>> test.rma<-rma(test.Dat) >>>>>>>>>> Background correcting >>>>>>>>>> Normalizing >>>>>>>>>> Calculating Expression >>>>>>>>>> >>>>>>>>>> #Extracting gcRMA assay data >>>>>>>>>>> test.gcrma.MAT<-exprs(test.gcrma) >>>>>>>>>>> dim(test.gcrma.MAT) >>>>>>>>>> [1] 15611 4 >>>>>>>>>> >>>>>>>>>> #Extracting RMA assay data >>>>>>>>>> >>>>>>>>>>> test.rma.MAT<-exprs(test.rma) >>>>>>>>>>> dim(test.rma.MAT) >>>>>>>>>> [1] 15611 4 >>>>>>>>>> >>>>>>>>>> #Running LPE function on gcRMA data and the resulting error >>>>>>>>>>> var.test.gcrma<-baseOlig.error(test.gcrma.MAT, q= 0.01) >>>>>>>>>> Error in var.M.adap[i] <- ifelse(!is.na(var.M.adap[i - 1]), >>>>>>>>>> mean(var.M.adap[i + : >>>>>>>>>> replacement has length zero >>>>>>>>>> >>>>>>>>>> #Running LPE function on RMA data - it successfully completes >>>>>>>>>>> var.test.rma<-baseOlig.error(test.rma.MAT, q= 0.01) >>>>>>>>>>> >>>>>>>>>> >>>>>>>>>> #My session info >>>>>>>>>>> sessionInfo() >>>>>>>>>> R version 2.8.0 (2008-10-20) >>>>>>>>>> i386-apple-darwin8.11.1 >>>>>>>>>> >>>>>>>>>> locale: >>>>>>>>>> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 >>>>>>>>>> >>>>>>>>>> attached base packages: >>>>>>>>>> [1] splines tools stats graphics grDevices utils >>>>>>>>>> datasets methods base >>>>>>>>>> >>>>>>>>>> other attached packages: >>>>>>>>>> [1] xenopuslaevisprobe_2.3.0 xenopuslaeviscdf_2.3.0 >>>>>>>>>> LPE_1.16.0 gcrma_2.14.0 >>>>>>>>>> matchprobes_1.14.0 affy_1.20.0 Biobase_2.2.0 >>>>>>>>>> >>>>>>>>>> loaded via a namespace (and not attached): >>>>>>>>>> [1] affyio_1.10.0 preprocessCore_1.4.0 >>>>>>>>>> >>>>>>>>>> Thanks a lot for your help >>>>>>>>>> >>>>>>>>>> Charlie >>>>>>>>>> >>>>>>>>>> >>>>>> ------------------------------------------------------------------- >>>>>>>>>> --------- >>>>>>>>>> >>>>>>>>>> Charlie Whittaker, Ph.D. >>>>>>>>>> Bioinformatics and Computing Core Facility The David H. Koch >>>>>>>>>> Institute for Integrative Cancer Research At MIT >>>>>>>>>> 77 Mass Ave E18-366 >>>>>>>>>> Cambridge, MA 02139 >>>>>>>>>> >>>>>>>>>> 617-324-0337 >>>>>>>>>> >>>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Bioconductor mailing list >>>>>> Bioconductor at stat.math.ethz.ch >>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>> Search the archives: >>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>>> >>>>>> >>>>> >>>>> _______________________________________________ >>>>> Bioconductor mailing list >>>>> Bioconductor at stat.math.ethz.ch >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>> Search the archives: >>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at stat.math.ethz.ch >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD REPLYlink written 10.8 years ago by Loren Engrav1.0k
Dear gcrma users, The reason for LPE error following gcrma is because gcrma shrinks some values to the same lower bound, if it appears to be indistinguishable from background distribution. In earlier versions of gcrma, the GSB.adjust step was performed on all probes after background adjustment, and since GSB.adjsut is slightly different array to array, the final values for each gene will not be identical even if the gene appears to be not expressed. In recent versions we stopped performing GSB.adjust for those values that appear to be indistinguishable from background (thus have no specific binding), following the suggestion in the paper by Lim et al (omparative analysis of microarray normalization procedures: effects on reverse engineering gene networks, Bioinformatics 2007 23(13)). I do not think it is an error or something that should be avoided to have identical values for some genes across all samples: if these genes or targets appear to be well within background in all samples, then probably the best thing to do is to acknowledge that their specific signal is 0 in all samples. In gcrma we used a small lower bound instead of 0 to avoid -inf in log transformation. Maybe LPE can have a check on 0 sample variance it has trouble handling genes with 0 variance right now. Or, possibly a prior on variance distribution can be introduced? best wishes Jean Wu Wolfgang Huber huber at ebi.ac.uk Tue Nov 4 11:47:28 CET 2008 * Previous message: [BioC] converting MA to a text file * Next message: [BioC] LPE error caused by gcRMA [Error in var.M.adap[i] <- ifelse(!is.na(var.M.adap[i - 1]), mean(var.M.adap[i + : replacement has length zero] * Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] Dear Charlie, I agree a lot with you that this is troublesome... but I would be interested in discussing (i) do you (and others) consider this an "error", or rather "bad behaviour" or "poor performance"? (ii) and is it gcrma, or LPE that errs or poorly performs? (iii) and are any of the maintainers of these packages interested in these questions? Best wishes Wolfgang
ADD REPLYlink written 10.8 years ago by Zhijin Wu260
Dear Jean thanks for the explanations! > Dear gcrma users, > > The reason for LPE error following gcrma is because gcrma shrinks some > values to the same lower bound, if it appears to be indistinguishable > from background distribution. In earlier versions of gcrma, the > GSB.adjust step was performed on all probes after background adjustment, > and since GSB.adjsut is slightly different array to array, the final > values for each gene will not be identical even if the gene appears to > be not expressed. > > In recent versions we stopped performing GSB.adjust for those values > that appear to be indistinguishable from background (thus have no > specific binding), following the suggestion in the paper by Lim et al > (omparative analysis of microarray normalization procedures: effects on > reverse engineering gene networks, Bioinformatics 2007 23(13)). > > I do not think it is an error or something that should be avoided to > have identical values for some genes across all samples: if these genes > or targets appear to be well within background in all samples, then > probably the best thing to do is to acknowledge that their specific > signal is 0 in all samples. In gcrma we used a small lower bound instead > of 0 to avoid -inf in log transformation. > > Maybe LPE can have a check on 0 sample variance it has trouble handling > genes with 0 variance right now. this would only work if the gene's value is shrunk to that magic minimal number for all arrays - and would not if shrunk for some but not for other arrays. > Or, possibly a prior on variance > distribution can be introduced? That might seem reasonable, yet perhaps isn't it a little convoluted to first shrink your estimate (in gcrma, using a heuristic) and then ask people to blow it up again (in virtually all subsequent differential expression computations, like LPE), using another heuristic. In particular, since the additive-multiplicative error model of Rocke and Durbin has proven to be extremely useful in for microarray data, wouldn't it be better to use that, and then properly propagate the estimated uncertainty from there, rather than asking LPE et al. to make up ad hoc uncertainty estimates? Best wishes Wolfgang ---------------------------------------------------- Wolfgang Huber, EMBL-EBI, http://www.ebi.ac.uk/huber > > best wishes > Jean Wu > > Wolfgang Huber huber at ebi.ac.uk > Tue Nov 4 11:47:28 CET 2008 > > * Previous message: [BioC] converting MA to a text file > * Next message: [BioC] LPE error caused by gcRMA [Error in > var.M.adap[i] <- ifelse(!is.na(var.M.adap[i - 1]), mean(var.M.adap[i + : > replacement has length zero] > * Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] > > Dear Charlie, > > I agree a lot with you that this is troublesome... but I would be > interested in discussing > > (i) do you (and others) consider this an "error", or rather "bad > behaviour" or "poor performance"? > > (ii) and is it gcrma, or LPE that errs or poorly performs? > > (iii) and are any of the maintainers of these packages interested in > these questions? > > Best wishes > Wolfgang >
ADD REPLYlink written 10.8 years ago by Wolfgang Huber13k
Hi, I just got around to digging into Guido's information on this thread. This LPE error happens with the gcrma argument: "fast=TRUE" but LPE works just fine when: "fast=FALSE" Unless I'm reading it wrong, according to the 10-31-08 gcrma vignette, the default setting for gcRMA is: "fast=FALSE": ------------------- 3. fast When fast is set to TRUE, an ad hoc procedure is used to speed up the non-speci?c binding correction. The default in previous version has been fast=TRUE , but is changed to fast=FALSE in version 2.0.0. ------------------- That leaves me a little unsure that this is the source of my problem. If my troubles are caused by fast=TRUE, the default gcRMA should be fine but it isn't. just to summarize: gcrma(x) = LPE error gcrma(x,fast=TRUE) = LPE error gcrma(x,fast=FALSE) = no LPE error in any case, fast=FALSE gets me moving again. Thanks a lot for the help. charlie On Nov 4, 2008, at 6:51 AM, Hooiveld, Guido wrote: > > Hi, > > Just to confirm that I and others also observed that since recently > GCRMA (>v 2.12) produces identical values for many probesets. > See e.g.: > http://thread.gmane.org/gmane.science.biology.informatics.conductor/ 1884 > 4/focus=18914 > This behaviour is related to a modification in how Gene Specific > Background (GSB) is handled in GCRMA v2.12, compared to previous > versions. > > G > >> -----Original Message----- >> From: bioconductor-bounces at stat.math.ethz.ch >> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of charliew >> Sent: 04 November 2008 12:12 >> To: Wolfgang Huber >> Cc: bioconductor at stat.math.ethz.ch >> Subject: Re: [BioC] LPE error caused by gcRMA [Error >> invar.M.adap[i] <- ifelse(!is.na(var.M.adap[i - >> 1]),mean(var.M.adap[i + : replacement has length zero] >> >> Hi Wolfgang, >> >>> (i) do you (and others) consider this an "error", or rather "bad >>> behaviour" or "poor performance"? >> >> I'd have to say it is an error because I feel like it should >> work but it doesn't. Although it is also bad behaviour and >> poor performance. >> >>> (ii) and is it gcrma, or LPE that errs or poorly performs? >> >> I don't really know. Both packages can work fine. >> >> LPE works great for RMA data or any other data matrices from >> different array platforms. It just does not work on any gcRMA >> data that I have tried. >> >> gcRMA produces very reasonable summarized data so it seems to >> work fine too. >> >> things break down when I try to take gcRMA data to LPE. I >> feel like it has something to do with rows that have >> identical values in all lanes. >> I think that might be a newer "feature" of gcRMA but I'm not sure. >> >> The context of this question is I have a batch of old array >> data that is being prepped for publication. >> Back in early 2006 I identified a set of potentially >> differentially expressed genes by summarizing the data with >> gcRMA, then diff testing with LPE. >> >> Unfortunately I didn't note versions of software and whatnot. >> Totally my fault. >> >> To gather the information I needed to write a good methods >> section, I wanted to repeat the analysis right now and more >> carefully document what I did. >> Trouble is, I get this error out of LPE and that is making it >> hard to exactly duplicate the old results. >> >> One thing I know for sure is the old and new gcRMA data are >> not identical so that lead me to think that a gcRMA change is >> the source of the problem. >> >>> (iii) and are any of the maintainers of these packages >> interested in >>> these questions? >> >> hopefully... >> >>> Best wishes >>> Wolfgang >>> >>> ------------------------------------------------------------------ >>> Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber >>> >>> >>> 31/10/2008 20:05 charliew scripsit >>>> Hi Patrick, >>>> Thanks a lot for the quick reply. I updated the package >> and it didn't >>>> fix the error. >>>> >>>> c >>>> On Oct 31, 2008, at 3:29 PM, Patrick Aboyoun wrote: >>>> >>>>> Charlie, >>>>> I don't know if this is related to you issue, but a bug >> in the gcrma >>>>> package was just fixed and there is a version 2.14.1 is now up on >>>>> bioconductor.org. Update to the latest version of gcrma >> and see if >>>>> it addresses your issue. >>>>> >>>>> >>>>> Patrick >>>>> >>>>> >>>>> >>>>> charliew wrote: >>>>>> Dear List, >>>>>> I've encountered the following error when running LPE: >>>>>> >>>>>> Error in var.M.adap[i] <- ifelse(!is.na(var.M.adap[i - 1]), >>>>>> mean(var.M.adap[i + : >>>>>> replacement has length zero >>>>>> >>>>>> It happens when the CEL files have been processed with gcRMA but >>>>>> not when they have been processed with RMA. >>>>>> I'm not positive about this but I think this error first started >>>>>> happening with the upgrade to gcRMA 2.x I think it is happening >>>>>> because gcRMA is producing a lot of probes with identical >>>>>> expression values. >>>>>> >>>>>> Here is a test session that causes the error. Upon request I can >>>>>> provide a tarball of the test data but any collection of >> CEL files >>>>>> will reproduce the error. >>>>>> The error also occurs if you run gcRMA from within >> onecolorGUI or >>>>>> affylmGUI. >>>>>> It also happens if you first write the expression data to a file >>>>>> with write.exprs, then read it back in with read.table. >>>>>> >>>>>> #Loading the packages >>>>>>> library(affy) >>>>>> Loading required package: Biobase >>>>>> Loading required package: tools >>>>>> >>>>>>> library(gcrma) >>>>>> Loading required package: matchprobes Loading required package: >>>>>> splines >>>>>> >>>>>>> library(LPE) >>>>>>> set.seed(0) >>>>>> >>>>>> #Reading in 4 CEL files >>>>>>> test.Dat<-ReadAffy() >>>>>> >>>>>> #Summarizing with gcRMA >>>>>>> test.gcrma<-gcrma(test.Dat) >>>>>> Adjusting for non-specific binding....Done. >>>>>> Normalizing >>>>>> Calculating Expression >>>>>> >>>>>> #Summarizing with RMA >>>>>>> test.rma<-rma(test.Dat) >>>>>> Background correcting >>>>>> Normalizing >>>>>> Calculating Expression >>>>>> >>>>>> #Extracting gcRMA assay data >>>>>>> test.gcrma.MAT<-exprs(test.gcrma) >>>>>>> dim(test.gcrma.MAT) >>>>>> [1] 15611 4 >>>>>> >>>>>> #Extracting RMA assay data >>>>>> >>>>>>> test.rma.MAT<-exprs(test.rma) >>>>>>> dim(test.rma.MAT) >>>>>> [1] 15611 4 >>>>>> >>>>>> #Running LPE function on gcRMA data and the resulting error >>>>>>> var.test.gcrma<-baseOlig.error(test.gcrma.MAT, q= 0.01) >>>>>> Error in var.M.adap[i] <- ifelse(!is.na(var.M.adap[i - 1]), >>>>>> mean(var.M.adap[i + : >>>>>> replacement has length zero >>>>>> >>>>>> #Running LPE function on RMA data - it successfully completes >>>>>>> var.test.rma<-baseOlig.error(test.rma.MAT, q= 0.01) >>>>>>> >>>>>> >>>>>> #My session info >>>>>>> sessionInfo() >>>>>> R version 2.8.0 (2008-10-20) >>>>>> i386-apple-darwin8.11.1 >>>>>> >>>>>> locale: >>>>>> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 >>>>>> >>>>>> attached base packages: >>>>>> [1] splines tools stats graphics grDevices utils >>>>>> datasets methods base >>>>>> >>>>>> other attached packages: >>>>>> [1] xenopuslaevisprobe_2.3.0 xenopuslaeviscdf_2.3.0 >>>>>> LPE_1.16.0 gcrma_2.14.0 >>>>>> matchprobes_1.14.0 affy_1.20.0 Biobase_2.2.0 >>>>>> >>>>>> loaded via a namespace (and not attached): >>>>>> [1] affyio_1.10.0 preprocessCore_1.4.0 >>>>>> >>>>>> Thanks a lot for your help >>>>>> >>>>>> Charlie >>>>>> >>>>>> >> ------------------------------------------------------------------- >>>>>> --------- >>>>>> >>>>>> Charlie Whittaker, Ph.D. >>>>>> Bioinformatics and Computing Core Facility The David H. Koch >>>>>> Institute for Integrative Cancer Research At MIT >>>>>> 77 Mass Ave E18-366 >>>>>> Cambridge, MA 02139 >>>>>> >>>>>> 617-324-0337 >>>>>> >>> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >
ADD REPLYlink written 10.8 years ago by Charlie Whittaker70
Charlie Looks like the vignette is wrong. You can see the default values by typing gcrma at the command prompt, or ?gcrma. Default for fast is TRUE, at least in version 2.14.1. Richard. charliew wrote: > Hi, > I just got around to digging into Guido's information on this thread. > > This LPE error happens with the gcrma argument: "fast=TRUE" > > but LPE works just fine when: "fast=FALSE" > > Unless I'm reading it wrong, according to the 10-31-08 gcrma vignette, > the default setting for gcRMA is: "fast=FALSE": > ------------------- > 3. fast > When fast is set to TRUE, an ad hoc procedure is used to speed up the > non-speci?c > binding correction. The default in previous version has been fast=TRUE , > but is > changed to fast=FALSE in version 2.0.0. > ------------------- > > That leaves me a little unsure that this is the source of my problem. > If my troubles are caused by fast=TRUE, the default gcRMA should be fine > but it isn't. > > just to summarize: > > gcrma(x) = LPE error > gcrma(x,fast=TRUE) = LPE error > gcrma(x,fast=FALSE) = no LPE error > > in any case, fast=FALSE gets me moving again. Thanks a lot for the help. > > charlie > > On Nov 4, 2008, at 6:51 AM, Hooiveld, Guido wrote: > >> >> Hi, >> >> Just to confirm that I and others also observed that since recently >> GCRMA (>v 2.12) produces identical values for many probesets. >> See e.g.: >> http://thread.gmane.org/gmane.science.biology.informatics.conductor /1884 >> 4/focus=18914 >> This behaviour is related to a modification in how Gene Specific >> Background (GSB) is handled in GCRMA v2.12, compared to previous >> versions. >> >> G >> >>> -----Original Message----- >>> From: bioconductor-bounces at stat.math.ethz.ch >>> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of charliew >>> Sent: 04 November 2008 12:12 >>> To: Wolfgang Huber >>> Cc: bioconductor at stat.math.ethz.ch >>> Subject: Re: [BioC] LPE error caused by gcRMA [Error >>> invar.M.adap[i] <- ifelse(!is.na(var.M.adap[i - >>> 1]),mean(var.M.adap[i + : replacement has length zero] >>> >>> Hi Wolfgang, >>> >>>> (i) do you (and others) consider this an "error", or rather "bad >>>> behaviour" or "poor performance"? >>> >>> I'd have to say it is an error because I feel like it should >>> work but it doesn't. Although it is also bad behaviour and >>> poor performance. >>> >>>> (ii) and is it gcrma, or LPE that errs or poorly performs? >>> >>> I don't really know. Both packages can work fine. >>> >>> LPE works great for RMA data or any other data matrices from >>> different array platforms. It just does not work on any gcRMA >>> data that I have tried. >>> >>> gcRMA produces very reasonable summarized data so it seems to >>> work fine too. >>> >>> things break down when I try to take gcRMA data to LPE. I >>> feel like it has something to do with rows that have >>> identical values in all lanes. >>> I think that might be a newer "feature" of gcRMA but I'm not sure. >>> >>> The context of this question is I have a batch of old array >>> data that is being prepped for publication. >>> Back in early 2006 I identified a set of potentially >>> differentially expressed genes by summarizing the data with >>> gcRMA, then diff testing with LPE. >>> >>> Unfortunately I didn't note versions of software and whatnot. >>> Totally my fault. >>> >>> To gather the information I needed to write a good methods >>> section, I wanted to repeat the analysis right now and more >>> carefully document what I did. >>> Trouble is, I get this error out of LPE and that is making it >>> hard to exactly duplicate the old results. >>> >>> One thing I know for sure is the old and new gcRMA data are >>> not identical so that lead me to think that a gcRMA change is >>> the source of the problem. >>> >>>> (iii) and are any of the maintainers of these packages >>> interested in >>>> these questions? >>> >>> hopefully... >>> >>>> Best wishes >>>> Wolfgang >>>> >>>> ------------------------------------------------------------------ >>>> Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber >>>> >>>> >>>> 31/10/2008 20:05 charliew scripsit >>>>> Hi Patrick, >>>>> Thanks a lot for the quick reply. I updated the package >>> and it didn't >>>>> fix the error. >>>>> >>>>> c >>>>> On Oct 31, 2008, at 3:29 PM, Patrick Aboyoun wrote: >>>>> >>>>>> Charlie, >>>>>> I don't know if this is related to you issue, but a bug >>> in the gcrma >>>>>> package was just fixed and there is a version 2.14.1 is now up on >>>>>> bioconductor.org. Update to the latest version of gcrma >>> and see if >>>>>> it addresses your issue. >>>>>> >>>>>> >>>>>> Patrick >>>>>> >>>>>> >>>>>> >>>>>> charliew wrote: >>>>>>> Dear List, >>>>>>> I've encountered the following error when running LPE: >>>>>>> >>>>>>> Error in var.M.adap[i] <- ifelse(!is.na(var.M.adap[i - 1]), >>>>>>> mean(var.M.adap[i + : >>>>>>> replacement has length zero >>>>>>> >>>>>>> It happens when the CEL files have been processed with gcRMA but >>>>>>> not when they have been processed with RMA. >>>>>>> I'm not positive about this but I think this error first started >>>>>>> happening with the upgrade to gcRMA 2.x I think it is happening >>>>>>> because gcRMA is producing a lot of probes with identical >>>>>>> expression values. >>>>>>> >>>>>>> Here is a test session that causes the error. Upon request I can >>>>>>> provide a tarball of the test data but any collection of >>> CEL files >>>>>>> will reproduce the error. >>>>>>> The error also occurs if you run gcRMA from within >>> onecolorGUI or >>>>>>> affylmGUI. >>>>>>> It also happens if you first write the expression data to a file >>>>>>> with write.exprs, then read it back in with read.table. >>>>>>> >>>>>>> #Loading the packages >>>>>>>> library(affy) >>>>>>> Loading required package: Biobase >>>>>>> Loading required package: tools >>>>>>> >>>>>>>> library(gcrma) >>>>>>> Loading required package: matchprobes Loading required package: >>>>>>> splines >>>>>>> >>>>>>>> library(LPE) >>>>>>>> set.seed(0) >>>>>>> >>>>>>> #Reading in 4 CEL files >>>>>>>> test.Dat<-ReadAffy() >>>>>>> >>>>>>> #Summarizing with gcRMA >>>>>>>> test.gcrma<-gcrma(test.Dat) >>>>>>> Adjusting for non-specific binding....Done. >>>>>>> Normalizing >>>>>>> Calculating Expression >>>>>>> >>>>>>> #Summarizing with RMA >>>>>>>> test.rma<-rma(test.Dat) >>>>>>> Background correcting >>>>>>> Normalizing >>>>>>> Calculating Expression >>>>>>> >>>>>>> #Extracting gcRMA assay data >>>>>>>> test.gcrma.MAT<-exprs(test.gcrma) >>>>>>>> dim(test.gcrma.MAT) >>>>>>> [1] 15611 4 >>>>>>> >>>>>>> #Extracting RMA assay data >>>>>>> >>>>>>>> test.rma.MAT<-exprs(test.rma) >>>>>>>> dim(test.rma.MAT) >>>>>>> [1] 15611 4 >>>>>>> >>>>>>> #Running LPE function on gcRMA data and the resulting error >>>>>>>> var.test.gcrma<-baseOlig.error(test.gcrma.MAT, q= 0.01) >>>>>>> Error in var.M.adap[i] <- ifelse(!is.na(var.M.adap[i - 1]), >>>>>>> mean(var.M.adap[i + : >>>>>>> replacement has length zero >>>>>>> >>>>>>> #Running LPE function on RMA data - it successfully completes >>>>>>>> var.test.rma<-baseOlig.error(test.rma.MAT, q= 0.01) >>>>>>>> >>>>>>> >>>>>>> #My session info >>>>>>>> sessionInfo() >>>>>>> R version 2.8.0 (2008-10-20) >>>>>>> i386-apple-darwin8.11.1 >>>>>>> >>>>>>> locale: >>>>>>> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 >>>>>>> >>>>>>> attached base packages: >>>>>>> [1] splines tools stats graphics grDevices utils >>>>>>> datasets methods base >>>>>>> >>>>>>> other attached packages: >>>>>>> [1] xenopuslaevisprobe_2.3.0 xenopuslaeviscdf_2.3.0 >>>>>>> LPE_1.16.0 gcrma_2.14.0 >>>>>>> matchprobes_1.14.0 affy_1.20.0 Biobase_2.2.0 >>>>>>> >>>>>>> loaded via a namespace (and not attached): >>>>>>> [1] affyio_1.10.0 preprocessCore_1.4.0 >>>>>>> >>>>>>> Thanks a lot for your help >>>>>>> >>>>>>> Charlie >>>>>>> >>>>>>> >>> ------------------------------------------------------------------- >>>>>>> --------- >>>>>>> >>>>>>> Charlie Whittaker, Ph.D. >>>>>>> Bioinformatics and Computing Core Facility The David H. Koch >>>>>>> Institute for Integrative Cancer Research At MIT >>>>>>> 77 Mass Ave E18-366 >>>>>>> Cambridge, MA 02139 >>>>>>> >>>>>>> 617-324-0337 >>>>>>> >>>> >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- Richard D. Pearson richard.pearson at postgrad.manchester.ac.uk School of Computer Science, http://www.cs.man.ac.uk/~pearsonr University of Manchester, Tel: +44 161 275 6178 Oxford Road, Mob: +44 7971 221181 Manchester M13 9PL, UK. Fax: +44 161 275 6204
ADD REPLYlink written 10.8 years ago by Richard Pearson390
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 256 users visited in the last hour