[BioC] serious problem with GOstats package

[Steve Lianoglou]

Hi,

On Wed, May 8, 2013 at 8:38 AM, gregory voisin <voisingreg at yahoo.fr> wrote:
> Hi,
>
> FOr my current analysis, I use GOstats package because it's a good, basic, simple package.
> I don't know why but since some time ,
>
> when I use this code:
>
> params <- new("GOHyperGParams", geneIds= sigLL, universeGeneIds = universeGeneIds , ontology=onto, pvalueCutoff= 0.01,conditional=FALSE,testDirection="over")
>
> hgOver <- hyperGTest(params)
>
> I have this error message:
>
>
> Erreur dans eapply(ID2GO(datPkg), function(goids) { :
>   erreur d'évaluation de l'argument 'env' lors de la sélection d'une méthode pour la fonction 'eapply' : Erreur dans (function (classes, fdef, mtable)  :
>   unable to find an inherited method for function ‘cols’ for signature ‘"function"’
>
> I have tested with R2.15.1, 2.12.! always the same problem. I think that the update of the package is sometimes problematic.

I'm guessing that a problem with the package is unlikely seeing as how
the vignette compiles (and recompiles almost nightly in devel(?)) just
fine.

My guess is that you are passing in some wonky params into the
function and perhaps you should look a bit more closely at what the
values of the geneIds, universeGeneIds, etc. are that you are sending
to the function.

-steve

--
Steve Lianoglou
Computational Biologist
Department of Bioinformatics and Computational Biology
Genentech