[LIMMA] change in normexp function between limma 2.2.0 to limma 2.4.4
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@gordon-smyth
Last seen 10 hours ago
WEHI, Melbourne, Australia
Dear Ron, If you type changeLog(n=100) in limma 2.4.4, you'll see that I made a couple of changes to normexp in limma 2.3.1 which apparently have not been very successful. Someone else asked the same question as you have a couple of weeks ago, see https://www.stat.math.ethz.ch/pipermail/bioconductor/2005-December/011 125.html Best wishes Gordon > Date: Wed, 14 Dec 2005 09:43:25 +0200 > From: "Ron Ophir" <ron.ophir at="" weizmann.ac.il=""> > Subject: [BioC] [LIMMA] change in normexp function between limma 2.2.0 > to limma 2.4.4 > To: <bioconductor at="" stat.math.ethz.ch=""> > Message-ID: <s39fe957.014 at="" wisemail.weizmann.ac.il=""> > Content-Type: text/plain; charset="us-ascii" > > Hi, > We have a microarray experiment of cDNA of 36 spotted arrays, reference > design. > Two persons run the analysis with same code and the same data for > education purposes. One loaded limma package version >>sessionInfo() > R version 2.2.0, 2005-10-06, i386-pc-mingw32 > > attached base packages: > [1] "methods" "stats" "graphics" "grDevices" "utils" > "datasets" > [7] "base" > > other attached packages: > limma > "2.4.4" > and the other >>sessionInfo() > R version 2.2.0, 2005-10-06, i386-pc-mingw32 > > attached base packages: > [1] "methods" "stats" "graphics" "grDevices" "utils" > "datasets" > [7] "base" > > other attached packages: > limma > "2.2.0" > > we run the following code: > > targets<-readTargets() > raw <- > read.images(targets=targets,format="genepix",wt.fun=wtflags(0.1)) > #genepix format > raw$genes<-readMyGAL() > png(file="densityPlotPreNormalized.png",width=800,height=400) > plotDensities(raw) > dev.off() > > RGb<-backgroundCorrect(raw, method="normexp", offset=50) > > png(file="densityPlotPreNormalizedBS.png",width=800,height=400) > plotDensities(RGb) > dev.off() > > data<-normalizeWithinArrays(RGb) # with background substraction > > png(file="densityPlotNormalized.png",width=800,height=400) > plotDensities(data) > dev.off() > >> max(raw$R) > [1] 63762 >> max(raw$G) > [1] 64016 > > for limma 2.4.4 >> max(RGb$R) > [1] 6.50953e+272 >> max(RGb$G) > [1] 3.146027e+248 > > for limma 2.2 > >> max(RGb_all$R) > [1] 63446.46 >> max(RGb_all$G) > [1] 63820.55 > > Where do you the problem might be? > > Thanks, > Ron > > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: densityPlotPreNormalized.png > Type: image/png > Size: 5985 bytes > Desc: not available > Url : > https://stat.ethz.ch/pipermail/bioconductor/attachments/20051214/666 58510/densityPlotPreNormalized-0001.png > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: densityPlotPreNormalizedBS2.4.png > Type: image/png > Size: 3008 bytes > Desc: not available > Url : > https://stat.ethz.ch/pipermail/bioconductor/attachments/20051214/666 58510/densityPlotPreNormalizedBS2.4-0001.png > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: densityPlotPreNormalizedBS2.2.png > Type: image/png > Size: 5979 bytes > Desc: not available > Url : > https://stat.ethz.ch/pipermail/bioconductor/attachments/20051214/666 58510/densityPlotPreNormalizedBS2.2-0001.png
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