Dear BioC listers,

I have a question regarding the preprocessing of the microarray data
(affymetrics HG-U133_Plus_2 chip) before sample classification. I was
wondering if summarization techniques might affect the performance of
classification methods. Has anyone experience with this? Or can someone give
suggestions whether (or when) to apply classification on the MAS 5.0, RMA,
GC-RMA or on the probe level data?

I realize that this might be a difficult question with no definite answer,
but some clues would already be helpful as it is a fundamental issue.

thanks in advance,
Willem Talloen





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