[BioC] hyperGTest and HyperGParams

[Robert Gentleman]

Hi,
   Sorry for the delay in responding.

  In a sense, you now always have a package, at least for organisms 
where there is a annotation package of the form org.Hs.eg.db, in your 
case you have two issues you need to deal with
  1) a map from Ensembl to EntrezGene (since that is the basis for that 
package). At some time, during this release cycle Ensembl ids are going 
to be added to that package so that you won't even need to do that soon.
  2) you need to decide what your universe is, and that is a problem 
typically, since it should reflect the genes you assayed, or could have 
detected.  Selecting this has an enormous effect on p-values so you 
should exercise some caution.

   params = new("GOHyperGParams", geneIds=myGenes,
              universeGeneIds=myUniverse,
              annotation="org.Hs.eg.db", ontology="BP",
              pvalueCutoff=0.01, conditional=FALSE,
              testDirection="over")

   hgOver = hyperGTest(params)

   which suitable choices for myGenes and myUniverse, should do what you 
want.


  best wishes
    Robert


João Fadista wrote:
> Dear all,
>  
> I would like to know if there is a way to use the hyperGTest function in the Category package if I don´t have an annotation package. I have the ensembl id´s of the genes in my microarray as well as all the GO terms associated with them.
>  
> If there is other tool that does the same job without the need of specifying the annotation package I will also be glad the hear about.
>  
>  
> Best regards,
> João Fadista
> 
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-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org