[BioC] Error in summary(hyperGtest)

Fraser Sim fjsim at buffalo.edu
Mon Jul 13 21:28:48 CEST 2009

I am using bioconductor to perform a hyperGtest on GO BP annotations. This
code has worked in the past but I am getting a strange error message from
the summary method of a hyperGtest-results object.

Here's the code:

> params = new("GOHyperGParams",
+    geneIds = as.numeric(geneIds),
+    universeGeneIds = as.numeric(GeneIDUniverse), annotation =
+    ontology = "BP", pvalueCutoff = 0.001, conditional = FALSE,
+    testDirection = "over")
> x <- hyperGTest(params)
> x
Gene to GO BP  test for over-representation 
652 GO BP ids tested (22 have p < 0.001)
Selected gene set size: 74 
    Gene universe size: 11847 
    Annotation package: hgu133plus2
> summary(x)
Error in if (nrow(df) == 0) { : argument is of length zero

Why does summary have this error when it looks like there are 22 categories
which should be returned?

Here's my sessionInfo()

R version 2.9.1 (2009-06-26) 

LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base     

other attached packages:
 [1] GOstats_2.10.0        graph_1.22.2          Category_2.10.1      
 [4] hgu133plus2.db_2.2.11 annaffy_1.16.0        KEGG.db_2.2.11       
 [7] GO.db_2.2.11          RSQLite_0.7-1         DBI_0.2-4            
[10] AnnotationDbi_1.6.1   limma_2.18.2          Biobase_2.4.1        

loaded via a namespace (and not attached):
[1] annotate_1.22.0   genefilter_1.24.2 GSEABase_1.6.0    RBGL_1.20.0      
[5] splines_2.9.1     survival_2.35-4   tools_2.9.1       XML_2.3-0        
[9] xtable_1.5-5     


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