Thank you, Sean!

Best,
     Allen

On Thu, Jul 10, 2008 at 11:24 AM, Sean Davis <sdavis2@mail.nih.gov> wrote:

> On Thu, Jul 10, 2008 at 11:05 AM, ss <affysnp@gmail.com> wrote:
> > Dear all,
> >
> > Hi! I have a question about using the function 'hyperGTest' in
> > GOstatsHyperG.
> > What if I want to find the enriched GO terms based on a set of genes
> which I
> > only know gene symbol, Ensembl Gene ID, and RefSeq ID. Since the array
> > is customized and I don't find the corresponding 'annotation' package in
> > Bioconductor.
> >
> > In other words, when making the:
> >
> > params <- new(...,geneIds, annotation,...), would it possible for me to
> pass
> > "gene symbol"
> > or "Ensembl Gene ID", or "RefSeq ID" to "geneIds" and ignore "annotation"
> > etc.?
>
> You can use the org.hs-type annotation package, which uses entrez gene
> id as the key.  So, you would need to get the Entrez Gene ID for the
> genes on your chip.  Given that you have RefSeq, Ensembl, and Symbol,
> you can use the same annotation package to get back to Entrez Gene ID
> from those other ID types.
>
> Sean
>

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