Hi Seth,
Thank you for your reply.

>> Hello

>> I am using hyperGTest to look at the GO enrichments. I am confused
>> with the output of the test. For a test, I took the genes in my
>> matrix, and found the those that map to GO:0009790 (there are 8 such
>> genes). Then I ran hyperGTest: using the 8 genes as the input, the
>> genes in my matrix as the universe genes (it is a subset of the
>> genes represented in the hgu133plus2 ).

> First, I'm a bit confused about what you are trying to accomplish.
> Usually, hyperGTest is used to find potentially interesting GO terms.
> Here it seems you are starting with a GO term of interest -- or are
> you just trying to understand/test hyperGTest?

Yes, I am trying to understand the output of the hyperGTest rather than starting with a GO term.

>But the GO::GOALLENTREZID map is odd in that it contains data across
>different organisms.  Why not instead:

> affyWithMyGO = hgu133plus2GO2ALLPROBES[["GO:0009790"]]
> egWithMyGO = unique(unlist(mget(affyWithMyGO, hgu133plus2ENTREZID)))

Intersection of 'egWithMyGO' with 'universeGenes' contains 31 genes.

> mygenes = intersect(egWithMyGO, universeGeneIds) 

When I run the hyperGTest...

> params = new("GOHyperGParams", geneIds = mygenes, universeGeneIds = universeGeneIds,
             annotation = "hgu133plus2",ontology = "BP", pvalueCutoff = 0.05,conditional = FALSE,testDirection = "over")

> hyp = hyperGTest(params)
> t = summary(hyp)

I get:

> t["GO:0009790",]
               GOBPID       Pvalue OddsRatio  ExpCount Count Size
GO:0009790 GO:0009790 4.455886e-60       Inf 0.9285024    31   31
                            Term
GO:0009790 embryonic development


This result does make sense, note that the Count and Size are the same, 31. We used 31 genes 
as input, got 31 back. So my question about hyperGTest is answered, I was just confused with the different number of genes.


Then my new question is why does 'GOALLENTREZID' contain only 8 genes associated with GO:0009790
 while 'egWithMyGO' obtained from 'hgu133plus2GO2ALLPROBES' contains more, i.e. 31 genes.
One would expect at least the same amount of genes in both environments or maybe more in 'GOALLENTREZID' because
affy chip does not represent all the genes?

best 
-burak






       
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