[BioC] Suggestions: process only a subset of affy data?

Cei Abreu-Goodger cei at sanger.ac.uk
Tue May 29 14:35:45 CEST 2007

Hello all,

I'm working with Affy GeneChips, and would like to know if anyone has 
suggestions regarding the following:

I will only be doing downstream analysis on a subset of the probes, for 
example: ~12,000 out of ~45,000 that I can actually map to a transcript 
with a 3'UTR.

- Would it make sense to normalize (or a 2nd normalization?) using only 
this subset of probes?

- Would it be better to use limma with the subset or the total set? I 
imagine the model would be more robust with all probes, but the p-value 
correction would then be more stringent.

Any pointers to other reading material would be greatly appreciated.



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