Hello, I just read a paper that I actually strongly recommend: "Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset" PMID 15693945 In this paper they advice to do 2 normalization steps, one after the background correction and one on the expression summary (using the loess method). I am not sure about how to do the latter (loess norm on the exp. summary). I have 2 conditions (say A and B) and triplicates (say A1, A2, A3 and B1, B2, B3). Once I get the expression summary: eset.mas = mas5(affybatch) How should I perform the loess normalization step? Thank you very much in advance for your help, Emmanuel