Hi, I'm working with custom slides(Cy5) and working in the normalization of the arrays. I have three arrays (technical replicates). I have sucesfully normalized the data using vsn, however i would like to compare it to the normalization using spike in controls. My controls are annotated as control-1 to x and i would like to do etiher a normalization by block per array or the mean of all the controls per array. Here is the code: library(limma) library(RColorBrewer) library(vsn) Cy5 <- "F635 Mean" Cy5b <- "B635 Mean" targets <- readTargets("targets.txt") #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$Gb <- NULL #Here are my spike in controls for normalization isSpikeIn <- grep("CTL", RG$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