[BioC] HyperGTest Gene Universe problem

Vivek Kaimal Vivek.Kaimal at cchmc.org
Mon May 7 05:40:36 CEST 2007

Hi Seth.

I am using the hyperGTest function for some genesets I have and I'm
having some problems with the Gene Universe & Gene set being used in the
analysis. My original Gene Universe contains 18382 genes and one of my
gene sets contains 597 genes. 
> length(GeneUniverse)
[1] 18382
> length(GeneList)
[1] 597

Then I run the following to test for over-representation:
> hgCutoff<-0.05
> params <- new("GOHyperGParams", geneIds = GeneList, universeGeneIds =
GeneUniverse,annotation = "hgu133plus2",ontology = "BP", pvalueCutoff =
hgCutoff, conditional = FALSE,testDirection = "over")
> hgOver <- hyperGTest(params)

But when I check the details for "hgOver", the number of genes used for
Gene Universe and Gene set seem to be much lower than my original sets.
The summary is as given below:

> hgOver
Gene to GO BP  test for over-representation 
1101 GO BP ids tested (160 have p < 0.05)
Selected gene set size: 427 
    Gene universe size: 11292 
    Annotation package: hgu133plus2 

Is it because some of my Entrez IDs are not being found in the
annotation package? Do I need to use another annotation package?

Thanks in advance.


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