Dear list,

I am trying to use GOstats using "under" and "over" testDirection. But,
the hyperGTest builds two diferent goDags. Shouldn't they be of the same
size??

Thanks,

Cristobal

> library(GOstats)
> load(file="Genes.RData"); genesModel <- out; rm(out)
> univer <- unique(as.character(genesModel$GeneID))
> paramsOver <- new("GOHyperGParams",
+   geneIds= univer[1:100],
+   universeGeneIds=univer[1:200],
+   annotation="org.Mm.eg.db",
+   ontology="BP",
+   pvalueCutoff=0.01,
+   conditional=FALSE,
+   testDirection="over")
Loading required package: org.Mm.eg.db

> paramsUnder <- new("GOHyperGParams",
+   geneIds= univer[1:100],
+   universeGeneIds=univer[1:200],
+   annotation="org.Mm.eg.db",
+   ontology="BP",
+   pvalueCutoff=0.01,
+   conditional=FALSE,
+   testDirection="under")

> over  <- hyperGTest(paramsOver)
> under <- hyperGTest(paramsUnder)
> over
Gene to GO BP  test for over-representation
1146 GO BP ids tested (0 have p < 0.01)
Selected gene set size: 80
    Gene universe size: 156
    Annotation package: org.Mm.eg
> under
Gene to GO BP  test for under-representation
1776 GO BP ids tested (0 have p < 0.01)
Selected gene set size: 80
    Gene universe size: 156
    Annotation package: org.Mm.eg
> length(pvalues(over))
[1] 1146
> length(pvalues(under))
[1] 1776

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