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...#My gpr files do only contain 1 channel (Cy5) RG <- read.maimages( targets$FileName,source="genepix",columns=list(R=Cy5,G=Cy5, Rb=Cy5b, Gb=Cy5b)) RG$G <- NULL RG$Gb <- NULL RG$genes <- readGAL("array_human_mirs.gal") #Here are my spike in controls for normalization isSpikeIn <- grep("CTL", RG$genes$Name) #The vsn normalization works fine mat <- vsnMatrix(RG$R) However i would like to normaliza using my spikein controls by block or by using the mean of all controls. Could you help on that ?? thanks, david [[alternative HTML version deleted]]