Thanks for the information, but I guess GOHyperG does not output the Gene
ontology term, while hyperGTest output both the GOid, as well as the  GO
term. However, my another question is how could I retrieve information about
the genes that have the enriched gene ontology (ie. which genes are
annotated with the enriched gene ontology)?

The hyperGTest gives us information about the count of the differentially
expressed genes that are annotated with that enriched gene ontology, and it
also gives the count of the genes in the array that are annotated with the
GO, but I would like to have information about which differentially
expressed genes are annotated with those GO. So I guess my question is given
a set of Locus link ID, is it possible to find the gene ontologies
associated with them by using the array's package : hgu133plus2 ?

(I tried to use GOLOCUSID2GO to find all the ontologies associated with each
of the differentially expressed genes, and see if each of the ontology is
enriched by looking back the result of the hyperGTest,  but I found the
results are not coherent; ie. the GO annotations of the package hgu133plus2
is not coherent with the result of the GOLOCUSID2GO )

So that's why I would like to retrieve the GO ids from a set of locus link
ids.

Appreciate for any help or comment



On 7/23/07, Seth Falcon <sfalcon@fhcrc.org> wrote:
>
> "Alex Tsoi" <tsoi.teen@gmail.com> writes:
>
> > Dear all,
> >
> > I am using GOHyperG to get the onverrepresented gene ontology of a set
> of
> > genes, and the results give the gene ontology IDs, I just wondering if I
> > could also get the gene ontology terms in the results ;
>
> What do you mean by terms?  Does the summary method on the test result
> do what you want?  Try:
>
>     ans <- hyperGTest(yourParams)
>     summary(ans)
>
> > and also, could someone shows me how I could get the gene ontology
> > terms from a set of gene ontology IDs ?
>
> Perhaps you want:
>
>    library("GO")
>    someGOTerms <- mget(someGOIDs, GOTERM)
>
> Have you had a look at the vignette that comes with GOstats?  Try:
>
>    library("GOstats")
>    openVignette(package="GOstats")
>
>
> + seth
>
> --
> Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research
> Center
> http://bioconductor.org
>



-- 
Lam C. Tsoi (Alex)
Medical University of South Carolina

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