[BioC] Newbie question on GOstats (hyperGTest) for dual channel (from SMD) arrays

[Marc Carlson]

Paul Evans wrote:
> Hi Marc,
>  
> Yes, the organism would be homo sapiens.
>  
>
>
>  
> ----- Original Message ----
> From: Marc Carlson <mcarlson at fhcrc.org>
> To: Paul Evans <p.evans48 at yahoo.com>
> Cc: Bioconductor at stat.math.ethz.ch
> Sent: Wednesday, March 26, 2008 12:05:20 PM
> Subject: Re: [BioC] Newbie question on GOstats (hyperGTest) for dual
> channel (from SMD) arrays
>
> Paul Evans wrote:
> > Hi,
> >
> > I had a microarray dataset (dual channel taken from Stanford
> Microarray Database) of 20,000 genes. I have used a filtering
> technique to reduce this to about 2500 genes. I now want to perform
> clustering and use the hyperGTest, as given in the GOstats:
> >
> >  hgCutoff <- 0.001
> >  params <- new("GOHyperGParams", geneIds = selectedEntrezIds,
> >  universeGeneIds = entrezUniverse, annotation = "hgu95av2",
> >  ontology = "BP", pvalueCutoff = hgCutoff, conditional = FALSE,
> >  testDirection = "over")
> >
> >
> > I understand that the universeGeneIds will be the entrez ids of the
> 2500 genes, and that the selectedEntrezIds are the entrez ids of the
> genes in a cluster, but what should I choose as the annotation
> package? I don't think the SMD gives the details of the array that was
> used.
> >
> > many thanks!
> >
> >
>

Then I would try to use the org.Hs.eg.db package.  This package provides
annotations for all the entrez gene IDs in Homo sapiens.

    Marc