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 /66658510/densityPlotPreNormalized.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 /66658510/densityPlotPreNormalizedBS2.4.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 /66658510/densityPlotPreNormalizedBS2.2.png