Different RMA expression values in different BioC versions?
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Quanli Wang ▴ 30
@quanli-wang-1990
Last seen 9.7 years ago
Dear Bioconductor community, We have been using justRMA to generate RMA values for some time. Recently we noticed that the latest versions of R(2.4.0/2.4.1) together with BioC(1.9) gave very different RMA expression values. Just wondering if anybody else has the similar experience. Thank you very much in advance for your help! Quanli Wang
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Ben Bolstad ★ 1.2k
@ben-bolstad-1494
Last seen 6.7 years ago
It would help if you could better quantify the exact size of the differences ("very different" is somewhat open to interpretation). I don't know if it is possible for you to reproduce this phenomenon again, but it would be helpful to verify that it is a problem. Also if it is feasible for you could you check the ReadAffy();rma() path just to ensure that it is a justRMA problem rather than something to do with the internal C rma code. Best, Ben > We have been using justRMA to generate RMA values for some time. Recently > we > noticed that the latest versions of R(2.4.0/2.4.1) together with BioC(1.9) > gave very different RMA expression values. Just wondering if anybody else > has > the similar experience. > > Thank you very much in advance for your help! > Quanli Wang >
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@james-w-macdonald-5106
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Quanli Wang wrote: > Dear Bioconductor community, > > We have been using justRMA to generate RMA values for some time. Recently we > noticed that the latest versions of R(2.4.0/2.4.1) together with BioC(1.9) > gave very different RMA expression values. Just wondering if anybody else has > the similar experience. Different than what? An earlier version with the same chips? What is the output from sessionInfo()? Jim > > Thank you very much in advance for your help! > Quanli Wang > > _______________________________________________ > 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 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
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> Different than what? An earlier version with the same chips? Yes. For the same chips using justRMA, the values from R2.3.1/BioC1.8 will be very different from that from R2.4.0/BioC1.9. Quanli
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Quanli Wang wrote: >>Different than what? An earlier version with the same chips? > > Yes. For the same chips using justRMA, the values from R2.3.1/BioC1.8 will > be very different from that from R2.4.0/BioC1.9. > Quanli I don't see that here. I get identical results for the same chips using these two versions of R/BioC > eset <- justRMA() Background correcting Normalizing Calculating Expression > save(eset, file="eset2.3.1.Rdata") > sessionInfo() Version 2.3.1 (2006-06-01) i386-pc-mingw32 attached base packages: [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" "datasets" [8] "base" other attached packages: hgu133plus2cdf affy affyio Biobase "1.12.0" "1.10.0" "1.0.0" "1.10.1" [close R-2.3.1, start R-2.4.0] > eset2 <- justRMA() Background correcting Normalizing Calculating Expression > load("eset2.3.1.Rdata") > all.equal(exprs(eset), exprs(eset2)) [1] TRUE > sessionInfo() R version 2.4.1 (2006-12-18) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] "tools" "stats" "graphics" "grDevices" "utils" "datasets" "methods" [8] "base" other attached packages: hgu133plus2cdf affy affyio Biobase "1.14.0" "1.12.2" "1.2.0" "1.12.2" Can you show the code you used to get different results, and the output of sessionInfo(), as requested in my last email? Best, Jim > > _______________________________________________ > 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 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
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Thank you all for the quick responses. Now seems that I figured out the problem. It has nothing todo with BioC but seems to me that it has something to do with the different implementations of "merge" function in R2.3.1 and R2.4.0. When I tried to reorder the expression values using merge function from R based on one prefered probeid list with "sort" option set to FALSE,R2.3.1 gives an order based on the x, while R2.4.0 gives an order based on y. Here is the little legacy script that does the ordering: eset <- read.table("eset.RData") geneID <- geneNames(eset) genedescriptorfile = "C:\\CAGP\\9999\\cel\\h133+.genedescriptors" genedes <- read.table(genedescriptorfile,sep="\t",header=FALSE, row.names=NULL) rmamatrix2 <- cbind(geneID,rmamatrix) cprmamatrix <- merge(x=rmamatrix2,y=genedes,by.x=1,by.y=1,all.x=FALSE,all.y=FALSE,sor t=FALSE) rmamatrix <- cprmamatrix[,2:ncol(rmamatrix2)] Can someone verify that it is indeed the case even it is more like an R problem, not a BioC problem. Best, Quanli On Wed, 10 Jan 2007, James W. MacDonald wrote: > Quanli Wang wrote: >>> Different than what? An earlier version with the same chips? >> >> Yes. For the same chips using justRMA, the values from R2.3.1/BioC1.8 will >> be very different from that from R2.4.0/BioC1.9. >> Quanli > > I don't see that here. I get identical results for the same chips using these > two versions of R/BioC > >> eset <- justRMA() > Background correcting > Normalizing > Calculating Expression >> save(eset, file="eset2.3.1.Rdata") >> sessionInfo() > Version 2.3.1 (2006-06-01) > i386-pc-mingw32 > > attached base packages: > [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" > "datasets" > [8] "base" > > other attached packages: > hgu133plus2cdf affy affyio Biobase > "1.12.0" "1.10.0" "1.0.0" "1.10.1" > > [close R-2.3.1, start R-2.4.0] > >> eset2 <- justRMA() > Background correcting > Normalizing > Calculating Expression >> load("eset2.3.1.Rdata") >> all.equal(exprs(eset), exprs(eset2)) > [1] TRUE >> sessionInfo() > R version 2.4.1 (2006-12-18) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > attached base packages: > [1] "tools" "stats" "graphics" "grDevices" "utils" "datasets" > "methods" > [8] "base" > > other attached packages: > hgu133plus2cdf affy affyio Biobase > "1.14.0" "1.12.2" "1.2.0" "1.12.2" > > Can you show the code you used to get different results, and the output of > sessionInfo(), as requested in my last email? > > Best, > > Jim > > >> >> _______________________________________________ >> 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 > > >
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