[BioC] FDR of enrichment analysis and other questions on GOstats

[Weiwei Shi]

Hi,

I read many previous posts and discussions over whether FDR
assessments should be applied or not on enrichment analysis (EA), here
I have two basic questions on that issue:

1. which packages provide ways to assess FDR when doing EA?
2. is there a way to provide customerized gene set defn. as input to
those packages? (another way to ask: which package allows customerized
gene set defn. as input?)

Mark:
I am interested in trying your described method of FDR on my dataset,
any share?


Seth:
I am intereted in knowing if inclusion or not of genes that have
little variation across samples has effect on ranks of significant
gene set? And how to choose or validate the cutoff to select expressed
genes? B/c it might be raised during paper review.

Thanks.

-- 
Weiwei Shi, Ph.D
Research Scientist
GeneGO, Inc.

"Did you always know?"
"No, I did not. But I believed..."
---Matrix III