Lumi warning and question
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Pan Du ★ 1.2k
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Hi Ingrid, I found you were still using the old lumi version 1.2.0. Due to the actively developing of lumi package, the latest version is 1.3.26. So please try the new version first and tell me this problem still exists. Thanks! Please check this link: http://www.bioconductor.org/packages/2.1/bioc/html/lumi.html Pan On 8/27/07 5:00 AM, "bioconductor-request at stat.math.ethz.ch" <bioconductor-request at="" stat.math.ethz.ch=""> wrote: > Message: 3 > Date: Mon, 27 Aug 2007 09:45:06 +0200 > From: Ingrid H. G. ?stensen <ingrid.h.g.ostensen at="" rr-research.no=""> > Subject: [BioC] Lumi warning and question > To: <bioconductor at="" stat.math.ethz.ch=""> > Message-ID: > <afe5b2464f1eb547bbace62cce8e40200b8118 at="" mr3k6001.ad.medicalresearch.no=""> > > Content-Type: text/plain > > Hi > > I have been using the lumi package for a while and I am currently using it on > 6 arrays (2 groups). I have gotten two warnings, that I have not seen before: > > dataSet <- lumiR(dataFil) > Warning message: > NAs introduced by coercion in: as.double.default(exprs) > > > jpeg(file = VST_plott,pointsize = 12, width = 650, height = 730) > plotVST(dataSet_T, main = "Data transformation") > Warning message: > NaNs produced in: log(x) > dev.off() > > I am also wondering about the number of "interestin" genes that are growing > after the background adjustment, transformation and normalization. Compare the > headings in figure 8 and 16 in the lumi vignette and you can see what I am > wondering about. > >> sessionInfo() > R version 2.5.1 (2007-06-27) > i386-pc-mingw32 > > locale: > LC_COLLATE=Norwegian (Bokm?l)_Norway.1252;LC_CTYPE=Norwegian > (Bokm?l)_Norway.1252;LC_MONETARY=Norwegian > (Bokm?l)_Norway.1252;LC_NUMERIC=C;LC_TIME=Norwegian (Bokm?l)_Norway.1252 > > attached base packages: > [1] "splines" "tools" "stats" "graphics" "grDevices" "utils" > "datasets" "methods" "base" > > other attached packages: > illuminaHumanv2 GOstats Category Matrix > lattice genefilter survival RBGL graph > "1.2.0" "2.2.6" "2.2.3" "0.999375-1" > "0.16-3" "1.14.1" "2.32" "1.12.0" "1.14.2" > annaffy KEGG GO xtable > RColorBrewer limma lumi annotate mgcv > "1.8.1" "1.16.1" "1.16.0" "1.5-1" > "1.0-1" "2.10.5" "1.2.0" "1.14.1" "1.3-26" > affy affyio Biobase > "1.14.2" "1.4.1" "1.14.1" > > > Regards, > Ingrid > --------------------------------------------------- Pan Du, PhD Research Associate / Senior Bioinformatics Analyst Robert H. Lurie Comprehensive Cancer Center Northwestern University 676 ST Clair St., #1200 Chicago, IL 60611 Office (312)695-4781 dupan at northwestern.edu
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Hi Ingrid, The problem here is you are using the devel version of lumi on a release version of R/BioC. If you want to use the devel version(s), you need to start with R-2.6.0devel and then install lumi using biocLite(). Best, Jim Ingrid H. G. ?stensen wrote: > Hi > > I got that part. :-) > > But how do I get the package? I tried the following: > >> source("http://bioconductor.org/biocLite.R") >> biocLite("AnnotationDbi") > Running biocinstall version 2.0.8 with R version 2.5.1 > Your version of R requires version 2.0 of Bioconductor. > Warning message: > package 'AnnotationDbi' is not available > > And I can not find int the BioC Release Packages (or am I blind at the moment?) > > Regards, > Ingrid > > You need to install ?AnnotationDbi? package, which is related with > ?annotate? package for the Bioconductor 2.1. Maybe you also need to install > some other packages related with the Bioconductor 2.1 update. Please check > the error message to see which package may be needed. > > Pan > > > On 8/27/07 9:00 AM, "Ingrid H. G. ?stensen" > <ingrid.h.g.ostensen at="" rr-research.no=""> wrote: > >> Hi >> >> I installed the new version and now I got error messages when I loaded the >> libraries: >> >>>> library(lumi) >> Loading required package: Biobase >> Loading required package: tools >> >> Welcome to Bioconductor >> >> Vignettes contain introductory material. To view, type >> 'openVignette()'. To cite Bioconductor, see >> 'citation("Biobase")' and for packages 'citation(pkgname)'. >> >> Loading required package: affy >> Loading required package: affyio >> Loading required package: mgcv >> This is mgcv 1.3-26 >> Loading required package: annotate >> Error in loadNamespace(name) : there is no package called 'AnnotationDbi' >> In addition: Warning message: >> package 'lumi' was built under R version 2.6.0 >> Error in as.environment(pos) : no item called "newtable" on the search list >>>> library(limma) >>>> library(RColorBrewer) >>>> library(xtable) >>>> library(annotate) >>>> library(annaffy) >> Loading required package: GO >> Loading required package: KEGG >>>> library(GOstats) >> Loading required package: graph >> Loading required package: RBGL >> Loading required package: Category >> Loading required package: genefilter >> Loading required package: survival >> Loading required package: splines >> Loading required package: Matrix >> Loading required package: lattice >>>> library(illuminaHumanv2) >>>> >>>> sessionInfo() >> R version 2.5.1 (2007-06-27) >> i386-pc-mingw32 >> >> locale: >> LC_COLLATE=Norwegian (Bokm?l)_Norway.1252;LC_CTYPE=Norwegian >> (Bokm?l)_Norway.1252;LC_MONETARY=Norwegian >> (Bokm?l)_Norway.1252;LC_NUMERIC=C;LC_TIME=Norwegian (Bokm?l)_Norway.1252 >> >> attached base packages: >> [1] "splines" "tools" "stats" "graphics" "grDevices" "utils" >> "datasets" "methods" "base" >> >> other attached packages: >> illuminaHumanv2 GOstats Category Matrix >> lattice genefilter survival RBGL graph >> "1.2.0" "2.2.6" "2.2.3" "0.999375-2" >> "0.16-3" "1.14.1" "2.32" "1.12.0" "1.14.2" >> annaffy KEGG GO xtable >> RColorBrewer limma annotate mgcv affy >> "1.8.1" "1.16.1" "1.16.0" "1.5-1" >> "1.0-1" "2.10.5" "1.14.1" "1.3-26" "1.14.2" >> affyio Biobase >> "1.4.1" "1.14.1" >> Regards, >> Ingrid >> >> >> >> Hi Ingrid, >> >> I found you were still using the old lumi version 1.2.0. Due to the actively >> developing of lumi package, the latest version is 1.3.26. So please try the >> new version first and tell me this problem still exists. Thanks! >> >> Please check this link: >> http://www.bioconductor.org/packages/2.1/bioc/html/lumi.html >> >> >> Pan >> >> >> On 8/27/07 5:00 AM, "bioconductor-request at stat.math.ethz.ch" >> <bioconductor-request at="" stat.math.ethz.ch=""> wrote: >> >>>> Message: 3 >>>> Date: Mon, 27 Aug 2007 09:45:06 +0200 >>>> From: Ingrid H. G. ?stensen <ingrid.h.g.ostensen at="" rr-="" research.no=""> >>>> Subject: [BioC] Lumi warning and question >>>> To: <bioconductor at="" stat.math.ethz.ch=""> >>>> Message-ID: >>>> <afe5b2464f1eb547bbace62cce8e40200b8118 at="" mr3k6001.ad.medicalresearch.no=""> >>>> >>>> Content-Type: text/plain >>>> >>>> Hi >>>> >>>> I have been using the lumi package for a while and I am currently using it >>> on >>>> 6 arrays (2 groups). I have gotten two warnings, that I have not seen >>> before: >>>> dataSet <- lumiR(dataFil) >>>> Warning message: >>>> NAs introduced by coercion in: as.double.default(exprs) >>>> >>>> >>>> jpeg(file = VST_plott,pointsize = 12, width = 650, height = 730) >>>> plotVST(dataSet_T, main = "Data transformation") >>>> Warning message: >>>> NaNs produced in: log(x) >>>> dev.off() >>>> >>>> I am also wondering about the number of "interestin" genes that are growing >>>> after the background adjustment, transformation and normalization. Compare >>> the >>>> headings in figure 8 and 16 in the lumi vignette and you can see what I am >>>> wondering about. >>>> >>>>>> sessionInfo() >>>> R version 2.5.1 (2007-06-27) >>>> i386-pc-mingw32 >>>> >>>> locale: >>>> LC_COLLATE=Norwegian (Bokm?l)_Norway.1252;LC_CTYPE=Norwegian >>>> (Bokm?l)_Norway.1252;LC_MONETARY=Norwegian >>>> (Bokm?l)_Norway.1252;LC_NUMERIC=C;LC_TIME=Norwegian (Bokm?l)_Norway.1252 >>>> >>>> attached base packages: >>>> [1] "splines" "tools" "stats" "graphics" "grDevices" "utils" >>>> "datasets" "methods" "base" >>>> >>>> other attached packages: >>>> illuminaHumanv2 GOstats Category Matrix >>>> lattice genefilter survival RBGL graph >>>> "1.2.0" "2.2.6" "2.2.3" "0.999375-1" >>>> "0.16-3" "1.14.1" "2.32" "1.12.0" "1.14.2" >>>> annaffy KEGG GO xtable >>>> RColorBrewer limma lumi annotate >>> mgcv >>>> "1.8.1" "1.16.1" "1.16.0" "1.5-1" >>>> "1.0-1" "2.10.5" "1.2.0" "1.14.1" "1.3-26" >>>> affy affyio Biobase >>>> "1.14.2" "1.4.1" "1.14.1" >>>> >>>> >>>> Regards, >>>> Ingrid >>>> >> > > > > > > [[alternative HTML version deleted]] > > > > -------------------------------------------------------------------- ---- > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623
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Hi It is most likely your second error is a result of the first error, fix that, the second error is likely to be fixed too. As for the difference in gene numbers in the clustering, it makes sense to me as you have tightened the std dev after normalization you will get greater difference between groups. It shouldn't take long to download R2.6 and update the required packages, I'd do the analysis again before giving them results! Cheers Alice -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor- bounces@stat.math.ethz.ch] On Behalf Of Ingrid H. G. ?stensen Sent: Tuesday, 28 August 2007 4:35 a.m. To: James W. MacDonald Cc: bioconductor at stat.math.ethz.ch; Pan Du Subject: Re: [BioC] Lumi warning and question Hmmmm, then I just have to see if I can put this testing into this weeks schedule. But the important issue here is: Do I have to call the researchers that I work for and tell them that their results will be delayed because I have to re-run the script when the source of the TWO warnings has been found, or is it okay to give them the results. (Have in mind that these results might lead to other projects or publications). And (again) has anyone any explanation to the increasing number of genes for the two plots in the lumi.pdf? Regards, Ingrid :-) Hi Ingrid, The problem here is you are using the devel version of lumi on a release version of R/BioC. If you want to use the devel version(s), you need to start with R-2.6.0devel and then install lumi using biocLite(). Best, Jim Ingrid H. G. ?stensen wrote: > Hi > > I got that part. :-) > > But how do I get the package? I tried the following: > >> source("http://bioconductor.org/biocLite.R") >> biocLite("AnnotationDbi") > Running biocinstall version 2.0.8 with R version 2.5.1 Your version of > R requires version 2.0 of Bioconductor. > Warning message: > package 'AnnotationDbi' is not available > > And I can not find int the BioC Release Packages (or am I blind at the > moment?) > > Regards, > Ingrid > > You need to install ?AnnotationDbi? package, which is related with > ?annotate? package for the Bioconductor 2.1. Maybe you also need to > install some other packages related with the Bioconductor 2.1 update. > Please check the error message to see which package may be needed. > > Pan > > > On 8/27/07 9:00 AM, "Ingrid H. G. ?stensen" > <ingrid.h.g.ostensen at="" rr-research.no=""> wrote: > >> Hi >> >> I installed the new version and now I got error messages when I >> loaded the >> libraries: >> >>>> library(lumi) >> Loading required package: Biobase >> Loading required package: tools >> >> Welcome to Bioconductor >> >> Vignettes contain introductory material. To view, type >> 'openVignette()'. To cite Bioconductor, see >> 'citation("Biobase")' and for packages 'citation(pkgname)'. >> >> Loading required package: affy >> Loading required package: affyio >> Loading required package: mgcv >> This is mgcv 1.3-26 >> Loading required package: annotate >> Error in loadNamespace(name) : there is no package called 'AnnotationDbi' >> In addition: Warning message: >> package 'lumi' was built under R version 2.6.0 Error in >> as.environment(pos) : no item called "newtable" on the search list >>>> library(limma) >>>> library(RColorBrewer) >>>> library(xtable) >>>> library(annotate) >>>> library(annaffy) >> Loading required package: GO >> Loading required package: KEGG >>>> library(GOstats) >> Loading required package: graph >> Loading required package: RBGL >> Loading required package: Category >> Loading required package: genefilter >> Loading required package: survival >> Loading required package: splines >> Loading required package: Matrix >> Loading required package: lattice >>>> library(illuminaHumanv2) >>>> >>>> sessionInfo() >> R version 2.5.1 (2007-06-27) >> i386-pc-mingw32 >> >> locale: >> LC_COLLATE=Norwegian (Bokm?l)_Norway.1252;LC_CTYPE=Norwegian >> (Bokm?l)_Norway.1252;LC_MONETARY=Norwegian >> (Bokm?l)_Norway.1252;LC_NUMERIC=C;LC_TIME=Norwegian >> (Bokm?l)_Norway.1252 >> >> attached base packages: >> [1] "splines" "tools" "stats" "graphics" "grDevices" "utils" >> "datasets" "methods" "base" >> >> other attached packages: >> illuminaHumanv2 GOstats Category Matrix >> lattice genefilter survival RBGL graph >> "1.2.0" "2.2.6" "2.2.3" "0.999375-2" >> "0.16-3" "1.14.1" "2.32" "1.12.0" "1.14.2" >> annaffy KEGG GO xtable >> RColorBrewer limma annotate mgcv affy >> "1.8.1" "1.16.1" "1.16.0" "1.5-1" >> "1.0-1" "2.10.5" "1.14.1" "1.3-26" "1.14.2" >> affyio Biobase >> "1.4.1" "1.14.1" >> Regards, >> Ingrid >> >> >> >> Hi Ingrid, >> >> I found you were still using the old lumi version 1.2.0. Due to the >> actively developing of lumi package, the latest version is 1.3.26. So >> please try the new version first and tell me this problem still exists. Thanks! >> >> Please check this link: >> http://www.bioconductor.org/packages/2.1/bioc/html/lumi.html >> >> >> Pan >> >> >> On 8/27/07 5:00 AM, "bioconductor-request at stat.math.ethz.ch" >> <bioconductor-request at="" stat.math.ethz.ch=""> wrote: >> >>>> Message: 3 >>>> Date: Mon, 27 Aug 2007 09:45:06 +0200 >>>> From: Ingrid H. G. ?stensen <ingrid.h.g.ostensen at="" rr-="" research.no=""> >>>> Subject: [BioC] Lumi warning and question >>>> To: <bioconductor at="" stat.math.ethz.ch=""> >>>> Message-ID: >>>> <afe5b2464f1eb547bbace62cce8e40200b8118 at="" mr3k6001.ad.medicalresearch="">>>> .no> >>>> >>>> Content-Type: text/plain >>>> >>>> Hi >>>> >>>> I have been using the lumi package for a while and I am currently >>>> using it >>> on >>>> 6 arrays (2 groups). I have gotten two warnings, that I have not >>>> seen >>> before: >>>> dataSet <- lumiR(dataFil) >>>> Warning message: >>>> NAs introduced by coercion in: as.double.default(exprs) >>>> >>>> >>>> jpeg(file = VST_plott,pointsize = 12, width = 650, height = 730) >>>> plotVST(dataSet_T, main = "Data transformation") Warning message: >>>> NaNs produced in: log(x) >>>> dev.off() >>>> >>>> I am also wondering about the number of "interestin" genes that are >>>> growing after the background adjustment, transformation and >>>> normalization. Compare >>> the >>>> headings in figure 8 and 16 in the lumi vignette and you can see >>>> what I am wondering about. >>>> >>>>>> sessionInfo() >>>> R version 2.5.1 (2007-06-27) >>>> i386-pc-mingw32 >>>> >>>> locale: >>>> LC_COLLATE=Norwegian (Bokm?l)_Norway.1252;LC_CTYPE=Norwegian >>>> (Bokm?l)_Norway.1252;LC_MONETARY=Norwegian >>>> (Bokm?l)_Norway.1252;LC_NUMERIC=C;LC_TIME=Norwegian >>>> (Bokm?l)_Norway.1252 >>>> >>>> attached base packages: >>>> [1] "splines" "tools" "stats" "graphics" "grDevices" "utils" >>>> "datasets" "methods" "base" >>>> >>>> other attached packages: >>>> illuminaHumanv2 GOstats Category Matrix >>>> lattice genefilter survival RBGL graph >>>> "1.2.0" "2.2.6" "2.2.3" "0.999375-1" >>>> "0.16-3" "1.14.1" "2.32" "1.12.0" "1.14.2" >>>> annaffy KEGG GO xtable >>>> RColorBrewer limma lumi annotate >>> mgcv >>>> "1.8.1" "1.16.1" "1.16.0" "1.5-1" >>>> "1.0-1" "2.10.5" "1.2.0" "1.14.1" "1.3-26" >>>> affy affyio Biobase >>>> "1.14.2" "1.4.1" "1.14.1" >>>> >>>> >>>> Regards, >>>> Ingrid >>>> >> > > > > > > [[alternative HTML version deleted]] > > > > ---------------------------------------------------------------------- > -- > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 [[alternative HTML version deleted]]
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