Hi All, I have microarray data coming from a Agilent custom shRNA library (3 controls "DMSO" and 3 treatments "DBZ"). To normalize these data I used the following code: library(limma) targets<-readTargets("targetfile_CycA100nM.txt") RG<-read.maimages(targets$FileName, source="agilent", ext="txt") MA<-MA.RG(RG, bc.method="none") RG.none<-backgroundCorrect (RG,method="none") MA.n<-normalizeWithinArrays(RG.none, method="loess") MA.Rq<-normalizeBetweenArrays(MA.n, method="quantile") By doing the correlation plot between the different samples I noticed that one sample (DBZ#1) looks weird. It seems that there is any correlation between this sample triplicates and between this sample and the control (see attachment). This is happening only with DBZ#1. On the other hand, by using GeneSpring software from Agilent this sample looks OK. Please, someone can help me into find out which is the error that I am doing in the script? Thank you very much, Giusy