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

[Cei Abreu-Goodger]

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.

Thanks!

Cei


The Wellcome Trust Sanger Institute is operated by Genome Research Limited,
a charity registered in England with number 1021457 and a company
registered in England with number 2742969, whose registered office is
215 Euston Road, London, NW1 2BE.