[BioC] Error in HyperGTest with GOHyperGParams class

[Pankaj Chopra]

Would it be possible to get a reproducible example?

thanks!

Mayte Suarez-Farinas wrote:
> Hi all,
> I recently updated to R 2.8. I have a list of significant genes and 
> want to do hypergeometric test to check for over-representing pathways 
> and ontologies.
> For KEGG it works fine but for GO I got the following error:
>
> any help will be appreciated!!!
>
>
>
> >params <- new("KEGGHyperGParams", geneIds = eids, universeGeneIds = 
> universe, annotation = lib, pvalueCutoff=1)
>
> > params2 <- new("GOHyperGParams", geneIds = eids, universeGeneIds = 
> universe,
> +           annotation = lib, ontology = ontology, conditional=cond, 
> pvalueCutoff=1)
>
>
> >  hyperGTest(params)
> Gene to KEGG  test for over-representation
> 116 KEGG ids tested (116 have p < 1)
> Selected gene set size: 139
>     Gene universe size: 3166
>     Annotation package: hgu133a2
>
> >     hyperGTest(params2)
> Error in initialize(value, ...) :
>   invalid names for slots of class "GOHyperGResult": pvalues, 
> oddsRatios, expectedCounts, catToGeneId
>
> >  str(params)
> Formal class 'KEGGHyperGParams' [package "Category"] with 8 slots
>   ..@ geneIds          : chr [1:394] "3608" "8882" "9948" "163" ...
>   ..@ universeGeneIds  : chr(0)
>   ..@ annotation       : chr "hgu133a2"
>   ..@ datPkg           :Formal class 'AffyDatPkg' [package "Category"] 
> with 1 slots
>   .. .. ..@ name: chr "hgu133a2"
>   ..@ cateogrySubsetIds: NULL
>   ..@ categoryName     : chr "KEGG"
>   ..@ pvalueCutoff     : num 1
>   ..@ testDirection    : chr "over"
>
> > str(params2)
> Formal class 'GOHyperGParams' [package "Category"] with 10 slots
>   ..@ ontology         : chr "BP"
>   ..@ conditional      : logi TRUE
>   ..@ geneIds          : chr [1:394] "3608" "8882" "9948" "163" ...
>   ..@ universeGeneIds  : chr(0)
>   ..@ annotation       : chr "hgu133a2"
>   ..@ datPkg           :Formal class 'AffyDatPkg' [package "Category"] 
> with 1 slots
>   .. .. ..@ name: chr "hgu133a2"
>   ..@ cateogrySubsetIds: NULL
>   ..@ categoryName     : chr "GO"
>   ..@ pvalueCutoff     : num 1
>   ..@ testDirection    : chr "over"
>
>
>
> sessionInfo()
> R version 2.8.1 (2008-12-22)
> i386-apple-darwin8.11.1
>
> locale:
> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] splines   tools     stats     graphics  grDevices utils     
> datasets  methods   base
>
> other attached packages:
>  [1] statmod_1.3.8            GOstats_2.8.0            
> RBGL_1.18.0              Category_2.8.4           annaffy_1.14.0
>  [6] KEGG.db_2.2.5            GO.db_2.2.5              
> hgu133a2probe_2.3.0      hgu133plus2.db_2.2.5     hgu133a2.db_2.2.5
> [11] hgu133a2cdf_2.3.0        Harshlight_1.12.0        
> altcdfenvs_2.4.0         hypergraph_1.14.0        graph_1.20.0
> [16] Biostrings_2.10.16       IRanges_1.0.12           
> makecdfenv_1.20.0        affyio_1.10.1            maCorrPlot_1.12.0
> [21] lumiHumanIDMapping_1.0.1 lumi_1.8.3               
> mgcv_1.4-1.1             affyQCReport_1.20.0      RColorBrewer_1.0-2
> [26] affyPLM_1.18.1           preprocessCore_1.4.0     
> simpleaffy_2.18.0        gcrma_2.14.1             matchprobes_1.14.1
> [31] genefilter_1.22.0        survival_2.34-1          
> affy_1.20.2              lumiHumanAll.db_1.4.0    RSQLite_0.7-1
> [36] DBI_0.2-4                beadarray_1.10.0         
> sma_0.5.15               hwriter_1.0              geneplotter_1.20.0
> [41] annotate_1.20.1          xtable_1.5-4             
> AnnotationDbi_1.4.3      lattice_0.17-17          Biobase_2.2.2
> [46] limma_2.16.4
>
> loaded via a namespace (and not attached):
> [1] GSEABase_1.4.0     KernSmooth_2.22-22 Matrix_0.999375-21 
> XML_2.1-0          cluster_1.11.11    grid_2.8.1
>
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