[BioC] using the hyperGTest function for E. coli genes

[Coghlan, Avril]

Dear all,

I am trying to use the hyperGTest function in the "GOStats" library to
test whether a particular set of E. coli genes has any particular GO
categories over-represented. I am having a little trouble figuring out
how to do this, and would appreciate advice very much.

I have two vectors containing lists of E. coli genes, "allgenes"
containing all E. coli genes, and "genes" containing a particular subset
of E. coli genes that I am interested in (and which I am suspect may be
enriched for certain GO categories).

I understand that I can use hyperGTest by typing something like this:

> params = new("GOHyperGParams", geneIds=genes,
universeGeneIds=allgenes, 
           annotation= "ECOLI", ontolog="BP", pvalueCutoff=0.001,
conditional=FALSE, 
           testDirection="over")
> mfhyper = hyperGTest(params)


However, I'm afraid this doesn't seem to work for me. I think that I
have the wrong thing in annotation="ECOLI", but I am not sure how to get
E. coli GO annotation. Most of the examples that I can find seem to use
human GO annotation data, which is already in Bioconductor. 

Do you know if I can get the E. coli GO annotation from Bioconductor
somehow, and if so, will I then be able to use the hyperGTest function
above?

I will be very grateful for help, I have been going around in circles a
little bit!

Kind regards,
Avril

Avril Coghlan
University College Cork, Ireland