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 Laboratoire de Biologie Moleculaire et Cellulaire du Cancer (LBMCC) Hopital Kirchberg 9,rue Edward steichen L-2540 LUXEMBOURG Phone:+ 352 2468-4046 Fax : + 352 2468-4060