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.


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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