Hi I am working on two color miRNA exiqon data, I could able to normalize data but the problem is once data is normalized my list contain 4 "within- array replicates" so I want make it to single miRNA's I tried to follow this thread "Read single channel GenePix in limma " by Gordon which works good for single channel data but when it come for two channel I am getting following error. Sequences of steps i am doing RG <- read.maimages(files, targets$FileName,columns=list(R="F635 Mean",G="F532 Mean",Rb="B635 Mean",Gb="B532 Mean")) dat <-normalizeBetweenArrays(RG, method="quantile") > dat2 <- log (dat) *Error in log(dat) : Non-numeric argument to mathematical function *rownames(dat@hx) <- RG.final$genes$Name* Error in rownames(dat@hx) <- RG.final$genes$Name : ---* this is basically where one can insert rownames into matrix with normalized data * no slot of name "hx" for this object of class "MAList" Any help is greatly appreciated Thanks Ashwin * [[alternative HTML version deleted]]