Hi, This might be very simple question, and I would like to confirm that what I am doing is wrong or right..!! here, what I do..: I have 6 CEL files, 3 Control and 3 Experimental. > myRMA<- rma(abatch); > MatrixRMA <- exprs(myRMA); > Group1_Raw_Mean_Intensity <- as.matrix(rowMeans(2^MatrixRMA[,1:3])); > Group2_Raw_Mean_Intensity <- as.matrix(rowMeans(2^MatrixRMA[,4:6])); Any help will help...!! Thank you, Saurin