[BioC] Gene Ontology - HyperGTest : Finding Significant terms

[Seth Falcon]

Hi Edward,

Edward Bolanger <ebolanger at yahoo.com> writes:
> Thanks for the reply and the helpful advice. I looked at some of the
> functions in GOstats and these are perhaps the ones that I
> need. Specifically, I am trying to use the 'HyperGTest' function.  I
> was looking at the document titled 'How To Use GOstats Testing Gene
> Lists for GO Term Association' to setup a new instance of
> GoHyperGParam'. The documentation says:'If you are using the YEAST
> annotation package, the vector will consist of FIXME.' 

Sorry for that.

> I'm not quite sure what I should put here. I tried using systemic
> names (e.g YER111C) for yeast genes but got the following error
> message:

I'm pretty sure you want to use the systematic names for these IDs
when using the YEAST package.  These are the IDs used as the keys in
the mappings in that annotation package.

>> params <- new("GOHyperGParams", geneIds = clust2,
> +         universeGeneIds = allGenes2, annotation = "YEAST", ontology
> + = "BP", pvalueCutoff = hgCutoff, conditional = FALSE, testDirection
> + = "over")
>>   hgOver <- hyperGTest(params)
> Error in getUniverseHelper(probes, lib, entrezIds) : No Entrez Gene
> ids left in universe

It is possible that you have used the correct IDs, but that there
aren't any annotations in GO BP...  Here is an example that works for
me:

    library("GOstats")
    library("YEAST")
    set.seed(434)    
    allYeast <- ls(YEASTCHR)
    selGenes <- sample(allYeast, 80)
    p <- new("GOHyperGParams",
             geneIds=selGenes,
             universeGeneIds=allYeast,
             ontology="BP",
             annotation="YEAST",
             pvalueCutoff=0.05,
             testDirection="over",
             conditional=FALSE)
    ans <- hyperGTest(p)


+ seth