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

[Mark W Kimpel]

Weiwie Shi,

I am happy to share whatever code I have, but mine is related to 
correcting for FDR in hyperGTest of package GOstats, not to GSEA. Is 
that what you are interested in?

Also, I never received any replies as to the advisability of actually 
doing this, so I can't say how others feel about it.

Let me know if you are interested, and I will post the code in a reply.

Mark

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Mark W. Kimpel MD  ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine

15032 Hunter Court, Westfield, IN  46074

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Weiwei Shi wrote:
> 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.
>