[BioC] Affymetrix: RMA probe summarization for identical probe sequences

Gaj Stan (BIGCAT) stan.gaj at maastrichtuniversity.nl
Wed Jul 20 15:45:38 CEST 2011

Hello all,

I have a very specific question regarding the working mechanisms behind the probe summarization step during RMA normalization. Let’s say that I have a reannotated probeset (customCDF) on an Affymetrix chip that looks like this: http://arrayanalysis.mbni.med.umich.edu/probeset/ps_pb.jsp?p=ENSG00000087076&c=HGU133Plus2_Hs_ENSG_13

This reannotated probeset seems to contain several identical probes, but these are located on a (physically) different location on the chip (although they’re not that far away from each other). How are these identical probes handled during the probe summarization step? As independant measurements? Averaged prior to summarization? Or anything else?

In the end, what effect would these repeated sequences have on the calculated (median-polished) probeset intensity? If I understand the approach correctly, it will not have a drastic effect on the outcome, since the assumption is that all probes in a given probeset should measure the same intensity...

Many thanks in advance!

  -- Stan

P.S.: I'm currently in disagreement with the BioC maillist settings. Therefore, my apologies if this post passed this list twice!

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