Hi, I have a question for the vsn normalization towards a reference data set. (my real data are much more) I will normalize 5 Arrays with vsn: ab_ref <- ReadAffy(filenames=celfiles[1:5]) fit_ref <- vsn2(ab_ref) After this I can add 2 Arrays with normalization towards a reference: ab_add <- ReadAffy(filenames=celfiles[6:7]) eSet1 <- vsnrma(ab_add, reference=fit_ref) And than I would like to add two more Arrays: ab_add2 <- ReadAffy(filenames=celfiles[7:8]) eSet2 <- vsnrma(ab_add2, reference=fit_ref) Do I use the old reference (fit_ref) for the second add-on normalization or the fit from the first add-on normalization or a combination of the first two fits? Thanks Markus -- Dipl.-Tech. Math. Markus Schmidberger Ludwig-Maximilians-Universit?t M?nchen IBE - Institut f?r medizinische Informationsverarbeitung, Biometrie und Epidemiologie Marchioninistr. 15, D-81377 Muenchen URL: http://www.ibe.med.uni-muenchen.de Mail: Markus.Schmidberger [at] ibe.med.uni-muenchen.de Tel: +49 (089) 7095 - 4497