[BioC] GOstats/Category hyperGTest gene universe problem

[James F. Reid]

Dear list,

when running two instances of a hyperGTest for KEGG pathways using 
different gene lists but identical gene universes I get two different 
gene universes in the results. This isn't the case for GO bp, mf, or cc 
but seems to be also for PFAM. Does anyone know why this is?

Thanks.
James.

Example and sessionInfo() below.

require("Category")
require("GOstats")
require("org.Hs.eg.db")

set.seed(321)

geneUniverse <- sample(mappedkeys(org.Hs.egSYMBOL), 2000)
geneList1 <- sample(geneUniverse, 200)
geneList2 <- sample(geneUniverse, 200)

## KEGG pathways
parsKEGG1 <- new("KEGGHyperGParams",
                 universeGeneIds = geneUniverse,
                 geneIds = geneList1,
                 annotation = "org.Hs.eg.db",
                 testDirection = "over",
                 pvalueCutoff = 0.01)
parsKEGG2 <- parsKEGG1
geneIds(parsKEGG2) <- geneList2

testKEGG1 <- hyperGTest(parsKEGG1)
testKEGG2 <- hyperGTest(parsKEGG2)
universeMappedCount(testKEGG1) == universeMappedCount(testKEGG2)
## [1] FALSE

universeMappedCount(testKEGG1)
## [1] 125
universeMappedCount(testKEGG2)
## [1] 137
sum(geneUniverse %in% mappedkeys(org.Hs.egPATH))
## [1] 213

## GO
parsGO1 <- new("GOHyperGParams",
                universeGeneIds = geneUniverse,
                geneIds = geneList1,
                annotation = "org.Hs.eg.db",
                conditional = TRUE,
                testDirection = "over",
                pvalueCutoff = 0.01)
parsGO2 <- parsGO1
geneIds(parsGO2) <- geneList2

## GO BP
ontology(parsGO1) <- ontology(parsGO2) <- "BP"
testGObp1 <- hyperGTest(parsGO1)
testGObp2 <- hyperGTest(parsGO2)
universeMappedCount(testGObp1) == universeMappedCount(testGObp2)
## [1] TRUE

## the same in CC and MF ontologies

sessionInfo()

R version 2.11.0 (2010-04-22)
x86_64-unknown-linux-gnu

locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
  [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] org.Hs.eg.db_2.4.1   GOstats_2.14.0       RSQLite_0.9-0
[4] DBI_0.2-5            graph_1.26.0         Category_2.14.0
[7] AnnotationDbi_1.10.1 Biobase_2.8.0

loaded via a namespace (and not attached):
[1] annotate_1.26.0   genefilter_1.30.0 GO.db_2.4.1       GSEABase_1.10.0
[5] RBGL_1.24.0       splines_2.11.0    survival_2.35-8   XML_3.1-0
[9] xtable_1.5-6