[BioC] probe level summarization before classification

[Naomi Altman]

It certainly affects differential expression analysis, so it is hard 
to imagine it will not affect clustering.

--Naomi

At 04:26 AM 2/20/2006, Talloen, Willem [PRDBE] wrote:
>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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>
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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111