[BioC] GOstats After Running Lumi

Shawn Westaway westaway at ohsu.edu
Fri May 11 02:20:07 CEST 2007

I am sorry, Seth and James, but I did not understand the universeGeneIds
command. Is this something I am supposed to generate from limma?

>>> "Seth Falcon" <sfalcon at fhcrc.org> - 5/3/07 8:22 PM >>>
"James W. MacDonald" <jmacdon at med.umich.edu> writes:
> First off, you are missing the universeGeneIds. I don't know what 
> hyperGTest will do in that situation, but it can't be as good as 
> actually specifying one.

If left unspecified, all genes probed on the chip are used as the
universe.  I fully agree that this is in most cases a suboptimal

+ seth

Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research

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