[BioC] serious problem with GOstats package

[Dan Tenenbaum]

On Thu, May 9, 2013 at 6:57 AM, gregory voisin <voisingreg at yahoo.fr> wrote:
> HI Dan
>
> My feeling about this problem is perhaps a not appropriate use of Gostat.
>
> Currently , I use Gostats with a package .db for lumi or affy...
>
> In the present case, i use Agilent platform and I don't specify the package(
> because it isn't existed) but I precise my geneUnivers.  This approach is it
> correct? Now, I'm not sure..I doubt
>
> Thanks for your help
>

I think James was right when he said you were missing the annotation argument?
Dan


> Greg
>
>
>
>
> ________________________________
> De : Dan Tenenbaum <dtenenba at fhcrc.org>
> À : gregory voisin <voisingreg at yahoo.fr>
> Cc : bioconductor <bioconductor at stat.math.ethz.ch>
> Envoyé le : Mercredi 8 mai 2013 19h12
> Objet : Re: [BioC] serious problem with GOstats package
>
> 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
>>>
>>        [[alternative HTML version deleted]]
>>
>>
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>