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 Charlie Whittaker
10.8 years ago by
Charlie Whittaker70 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 • 603 views
ADD COMMENTlink modified 10.8 years ago by Patrick Aboyoun1.6k • written 10.8 years ago by Charlie Whittaker70
Answer: LPE error caused by gcRMA [Error in var.M.adap[i] <- ifelse(!is.na(var.M.adap[i
0
gravatar for Patrick Aboyoun
10.8 years ago by
Patrick Aboyoun1.6k
United States
Patrick Aboyoun1.6k 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 COMMENTlink written 10.8 years ago by Patrick Aboyoun1.6k
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
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: 250 users visited in the last hour