[BioC] hyperGTest interpretation of 'under' and finding all Entrez associated with a GO term

[Steve Lianoglou]

Hi,

On Mon, Nov 12, 2012 at 12:28 PM, Mary Kindall <mary.kindall at gmail.com> wrote:
> Hi Steve
> Thanks for reply.
> I am able to find all Entrez for a particular GO term, however, the 'count'
> and 'size' of HyperGTest result do not match the numbers.
>
> For example, I got this as result of my HyperGTest.
>
> "GOBPID" "Pvalue" "OddsRatio" "ExpCount" "Count" "Size" "Term"
> "GO:0032501" "9.62590502703856e-31" "2.84380308273042" "116.003908034309"
> "235" "3975" "multicellular organismal process"
>
> count = 235
> Size = 3975
>
> When I do :
>> length(org.Mm.egGO2ALLEGS[["GO:0032501"]])
> [1] 8163
>> length(org.Mm.egGO2EG[["GO:0032501"]])
> [1] 0
>
> None of them equal to 3975.

What if you only take the subset of genes annotated with "GO:0032501"
that is in the universe you specified?

`org.Mm.egGO2ALLEGS[["GO:0032501"]]` will return all genes annotated
with this term in the "mouse universe".

In your previous email, it seems as if your background gene set is
stored in `uGenes`, so does:

length(intersect(org.Mm.egGO2ALLEGS[["GO:0032501"]], uGenes))

Get you closer?

-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact