[BioC] serious problem with GOstats package

[James W. MacDonald]

On 5/9/2013 10:29 AM, Dan Tenenbaum wrote:
> 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?

And in the case where there isn't a chip-specific .db package, you use 
the org.Xx.eg.db package. IIRC, these are human, so it would be 
org.Hs.eg.db.

Best,

Jim


> 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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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099