Hi,
I try to decide if my set of genes is down-regulated in one of my two samples by using function geneSetTest() in limma.

First, I did
fit2<-eBayes(fit2)
myGeneSetAffyID_index<-match(myGeneSetAffyID,fit2genes[,1])
myGeneSetAffyID_index<-myGeneSetAffyID_index[!is.na(myGeneSetAffyID_index)]
geneSetTest(myGeneSetAffyID_index,fit2$t[,1], "less")
I got p-value 0.0003, it is significant if I use cutoff p-value 0.05.

Then I tried another way by using unigene ID. I converted affyID into Unigene ID and tried geneSetTest again. What I did is like the following:
unigene<-unlist(as.list(hgu133aUNIGENE))
# in case one affyID map to multiple Unigene IDs, multiple Unigene IDs are separated by ";". But for my example, each affyID map to only one Unigene ID
myGeneSetUnigeneID<-as.character(unlist(lapply(mget(myGeneSetAffyID, env=hgu133aUNIGENE),function(unigeneId){ return(paste(unigeneID, collapse="; "))})))
myGeneSetUnigeneID_index<-match(myGeneSetUnigeneID, unigene)
myGeneSetUnigeneID_index<-myGeneSetUnigeneID_index[!is.na(myGeneSetUnigeneID_index)]
geneSetTest(myGeneSetUnigeneID_index, fit2$t[,1],"less")
I got p-value 0.4, and it is not significant.

I compare myGeneSetAffyID_index with myGeneSetUnigeneID_index, they are totally different, I think myGeneSetAffyID_index is the vector of indices of my gene set members in fit2$t, and myGeneSetUnigeneID_index is not. So I guess first p-value is correct. But I am not very sure. Could anyone help me about this?

If first p-value is correct, my gene set is significantly down-regulated. But when I use GSEA(gene set enrichment analysis program), the FDR I got is much larger than 0.25. My question here is whether p value from function geneSetTest is comparable to FDR from GSEA?

Thanks for any help!

Ren 

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