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

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. >