Hi,

We are trying to compare affymetrix genelists generated a while back
using MAS 5.0 to the new genelists generated using RMA analysis.
Previously, we used to perform a comparison expression analysis of the
replicates first (3 replicates for each condition) in order to determine the
false positive rate. Is there a way to do something similar in RMA just for
comparative purposes?
Also, is it possible to compare only 2 chips at a time and generate a
correlation coefficient? I checked the posting guide but couldn't find a
previous email that would answer this question.

Any help or pointing where to look is much appreciated,
Thanks,
Kai

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