[BioC] hyperGTest(GOstats) result question

[Seth Falcon]

Hi Burak,

burak kutlu <burak_kutlu at yahoo.com> writes:
> 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?

> When I look at the results, the count field is = 3. I would expect
> it to be 8. This probably changes the outcome. Am I missing
> something?

> I include the code below as well as the sessionInfo() output.
> Any help is appreciated.

I wonder if you could provide a reproducible example?  If you can send
me off list the myGenes and universeGenes, perhaps I can see what you
are seeing.

A few comments on your code below...

> universeGeneIds = rownames(myMatrix)
> genesWithMyGO = as.list(GOALLENTREZID)$'GO:0009790'

How about:

 genesWithMyGO = GOALLENTREZID[["GO:0009790"]]

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)))

> geneIds = intersect(genesWithMyGO, universeGeneIds) # there are 8 genes that are in my matrix with this GO id
>
>> geneIds
> [1] "3084"  "4683"  "5801"  "650"   "9314"  "89870" "2139"  "3216"
>
> params = new("GOHyperGParams", geneIds = mygenes, universeGeneIds =

Did you intend to use geneIds instead of mygenes here?
                               
> hyp = hyperGTest(params)
> t = summary(hyp)
> tRep = cbind(t$GOBPID,t$Pvalue,t$OddsRatio,t$ExpCount,t$Count,t$Size,t$Term)
> test = tRep[which(tRep[,1]=='GO:0009790'),] # enrichment result with this term
> names(test) = c(
> "GOBPID","Pvalue","OddsRatio","ExpCount","Count","Size","Term")

Why not:

 t["GO:0009790", ]

+ seth

-- 
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
http://bioconductor.org