[BioC] Suggestions: process only a subset of affy data?
cei at sanger.ac.uk
Tue May 29 14:35:45 CEST 2007
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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