[BioC] using GOstats hyperGTest without microarray annotation

Seth Falcon sfalcon at fhcrc.org
Tue Jun 12 18:36:42 CEST 2007

"marco zucchelli" <marco.bioc at gmail.com> writes:

> Dear Bioc,
>  can go stats be used without a microarray annotation, i.e. to test a set of
> genes against a specified universe?
>>From my understanding the GOHyperGParams accept a gene list, and a universe
> (as entrez names). So a this point hyperGTest should
> not use the the micorarray annotation anymore ?
> If this is not possible is there any other package for this kind of
> test ?

You can set the annotation to <what>LLMappings for <what> = human,
mouse, or rat.  The topGO package may also be of use to you.

+ seth

Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center

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