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

[Serge Eifes]

Dear Marc,

As I'im actually working with the Gostat package and don't know how to
implement correctly multiple hypothesis correction by FDR for the results
obtained I would be very glad if you could post the code previously
mentioned.
Many thanks in advance!

Best Regards,
Serge Eifes



>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
>
>---
>
>Mark W. Kimpel MD  ** Neuroinformatics ** Dept. of Psychiatry Indiana
University School of Medicine
>
>15032 Hunter Court, Westfield, IN  46074
>
>(317) 490-5129 Work, & Mobile & VoiceMail
>(317) 663-0513 Home (no voice mail please)
>
>******************************************************************
>
>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.
>>




Serge Eifes
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