[BioC] serious problem with GOstats package

[James W. MacDonald]

Hi Greg,

On 5/8/2013 11:38 AM, gregory voisin wrote:
> Hi,Â
>
> 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")

You are missing the annotation argument.

Best,

Jim


> Â
> hgOver<- hyperGTest(params)
>
> I have this error message:
>
>
> Erreur dans eapply(ID2GO(datPkg), function(goids) { :Â
>   erreur d'évaluation de l'argument 'env' lors de la sélection d'une méthode pour la fonction 'eapply' : Erreur dans (function (classes, fdef, mtable)  :Â
>   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)
>
> Â
>
> 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 Â LC_CTYPE=French_Canada.1252 Â  Â LC_MONETARY=French_Canada.1252
> [4] LC_NUMERIC=C Â  Â  Â  Â  Â  Â  Â  Â  Â  LC_TIME=French_Canada.1252 Â  Â
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods   base    Â
>
> other attached packages:
> Â [1] hgu95av2.db_2.9.0 Â  Â org.Hs.eg.db_2.9.0 Â  ALL_1.4.14 Â  Â  Â  Â  Â  topGO_2.12.0 Â  Â  Â  Â
> Â [5] SparseM_0.99 Â  Â  Â  Â  GO.db_2.9.0 Â  Â  Â  Â  Â GOstats_2.26.0 Â  Â  Â  RSQLite_0.11.3 Â  Â  Â
> Â [9] DBI_0.2-6 Â  Â  Â  Â  Â  Â graph_1.38.0 Â  Â  Â  Â  Category_2.26.0 Â  Â  Â AnnotationDbi_1.22.5
> [13] Biobase_2.20.0 Â  Â  Â  BiocGenerics_0.6.0 Â  limma_3.16.3 Â  Â  Â  Â  BiocInstaller_1.10.1
>
> loaded via a namespace (and not attached):
> Â [1] annotate_1.38.0 Â  Â  Â  AnnotationForge_1.2.1 genefilter_1.42.0 Â  Â  grid_3.0.0 Â  Â  Â  Â  Â Â
> Â [5] GSEABase_1.22.0 Â  Â  Â  IRanges_1.18.0 Â  Â  Â  Â lattice_0.20-15 Â  Â  Â  RBGL_1.36.2 Â  Â  Â  Â  Â
> Â [9] splines_3.0.0 Â  Â  Â  Â  stats4_3.0.0 Â  Â  Â  Â  Â survival_2.37-4 Â  Â  Â  tools_3.0.0 Â  Â  Â  Â  Â
> [13] XML_3.96-1.1 Â  Â  Â  Â  Â xtable_1.7-1 Â  Â  Â  Â Â
> 	[[alternative HTML version deleted]]
>
>
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099