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List:       bioconductor
Subject:    Re: [BioC] HyperGTest error question
From:       Seth Falcon <sfalcon () fhcrc ! org>
Date:       2007-03-28 1:14:52
Message-ID: m2odmeqicz.fsf () ziti ! fhcrc ! org
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Hi,

"Vivek Kaimal" <Vivek.Kaimal@cchmc.org> writes:

> Hi there,
>
> I'm trying to use the hyperGTest function. What I tried  is as
> follows:
>
>> params <- new("GOHyperGParams", geneIds = GList, universeGeneIds =
> geneUniverse, annotation = "hgu133plus2", ontology = "BP", pvalueCutoff
> = hgCutoff, conditional = FALSE,testDirection = "over")
>
> Both GList & geneUniverse contain genes in HUGO format (symbols).

You need to use Entrez IDs for the geneIds and universeGeneIds
argument.

+ seth

-- 
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
http://bioconductor.org


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