Dear list, I'm trying to better understand what the "affy.scalevalue.exprSet" function does exactly (affy package). I know it is normally used for MAS pre-processing, but I found it very useful in an RMA context, to kind of normalise different set of chips to the same "subset" that has been median polished 1st then used as a scale factor. When looking at the function in a prompt shell, I read "mean" although I thought this function was using the scale factor to scale up the medians and not the means. I'm not sure it would make a big difference anyway, but I just wondered, if I medpolish my subset, wouldn't it make more sense to continue using the medians? I noticed on the boxplots before and after the scaling that the intensities distribution vary and tend to be more equals on the upper limit of the quartiles after scaling up the chips, which is not what RMA does, or does it? Thank you very much for your time Celine -- Celine Carret PhD Pathogen Microarrays group The Wellcome Trust Sanger Institute Hinxton, Cambridge CB10 1SA, UK. tel. +44 (0)1223 494 940 fax. +44 (0)1223 494 919 email: ckc at sanger.ac.uk http://www.sanger.ac.uk/PostGenomics/PathogenArrays/