[BioC] Error in HyperGTest with GOHyperGParams class

[Mayte Suarez-Farinas]

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