[BioC] serious problem with GOstats package

[Dan Tenenbaum]

Hi Gregory,


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")

What are the values of sigLL, universeGeneIds, and onto?

Please post a complete reproducible example.

Thanks,
Dan


>
> 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.
>
>
> If you have a solution, a suggestion or an alternative ( I'm going to see topGO)
>
>
>
> Thanks for your help
>
>
>> sessionInfo()
> R version 3.0.0 (2013-04-03)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=French_Canada.1252  LC_CTYPE=French_Canada.1252    LC_MONETARY=French_Canada.1252
> [4] LC_NUMERIC=C                   LC_TIME=French_Canada.1252
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>  [1] hgu95av2.db_2.9.0    org.Hs.eg.db_2.9.0   ALL_1.4.14           topGO_2.12.0
>  [5] SparseM_0.99         GO.db_2.9.0          GOstats_2.26.0       RSQLite_0.11.3
>  [9] DBI_0.2-6            graph_1.38.0         Category_2.26.0      AnnotationDbi_1.22.5
> [13] Biobase_2.20.0       BiocGenerics_0.6.0   limma_3.16.3         BiocInstaller_1.10.1
>
> loaded via a namespace (and not attached):
>  [1] annotate_1.38.0       AnnotationForge_1.2.1 genefilter_1.42.0     grid_3.0.0
>  [5] GSEABase_1.22.0       IRanges_1.18.0        lattice_0.20-15       RBGL_1.36.2
>  [9] splines_3.0.0         stats4_3.0.0          survival_2.37-4       tools_3.0.0
> [13] XML_3.96-1.1          xtable_1.7-1
>>
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>
>
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