Hello all, I have a very specific question regarding the probe summarization step during Affymetrix MA normalisation. Let's say that I have a reannotated probeset (customCDF) that looks like this: http://arrayana lysis.mbni.med.umich.edu/probeset/ps_pb.jsp?p=ENSG00000087076&c=HGU133 Plus2_Hs_ENSG_13 This reannotated probeset seems to contain several identical probes, but they are located on a (physically) different location on the chip (although they're not that far away). How are these identical probes handled during the probe summarization step? As independant probes? Averaged prior to summarization? Or anything else? Best, -- Stan [[alternative HTML version deleted]]