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

[Marc Carlson]

Hi Avril,

We presently have two E. coli packages, but only one of them has any GO
data in it (this has to do with what was available when we made these
packages).  If your E. coli is a different strain than the common one,
you will have to find annotations that connect the gene IDs to the the
GO terms and use the AnnotationDbi package to create a custom package.

The E. coli package that has GO data is for the common lab strain (K12
strain) of E. coli.  This package is called "org.EcK12.eg.db".  If that
is the correct kind of E. coli, then you can proceed, and use that as
your annotation parameter.  However, you will also have to pay attention
to the fact that this package uses Entrez Gene IDs as the primary gene
identifiers for it's mappings (that is why it says "eg" in the name). 
So you will have to be also using entrez gene IDs as your identifiers
when you set up the params object.  Specifically "allGenes" and "genes"
will have to both be lists of Entrez Gene IDs to use this annotation
package in this way.

Please let me know if you have any more questions,


  Marc




Coghlan, Avril wrote:
> 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
>
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