Hi, I wish to use R to have the log(2) expressions of genes from a few cDNA samples (from layout: PMCI_10.5KSC_GP.gal). The experiment is done with a common reference, and dye swaps are carried out for different wild types too; for example: WildType A Test ref WildType A Ref Test Wild type B Test Ref Wild type B Test Ref Wild type B ref test ........... ...... ..... For this, although I was trying the following commands, but was unsure as to where and how I would integrate the above information. Also, I am not very sure and thus, please suggest how I can finally obtain the log2-expression values! Hope you would kindly reply. Thank you ! Cheers, Santana = = === = = = = = == = library(arrayQuality) targets <- readTargets("target.txt") files <- c("##.gpr", " ##.gpr" ..........) # file names are not written down RG <- read.maimages(files,source="genepix") RG$printer <- getLayout(RG$genes) RG.b <- backgroundCorrect(RG, method="none") library (convert) RG.Within <- normalizeWithinArrays (RG.b, method="loess") RG.Between <- normalizeBetweenArrays (RG.Within, method="quantile") genes <- RG.Between$genes log_ratios <- RG.Between$M Mean_LogIntensity <- RG.Between$A Log_Ratio_table <- cbind (genes,log_ratios) MeanLog_Intensity_table <- cbind (genes,Mean_LogIntensity) [[alternative HTML version deleted]]