Hi, Is the FDR assumed to be a certain percent (e.g. 5%) in the FDR adjustment for p values? If so, is it possible to change it? Are these FDR adjusted p-values the same as/similar to q-values in SAM procedure? Thanks in advance! Best regards, Fai ________ Yuk Fai Leung Bauer Center for Genomics Research Harvard University 7 Divinity Avenue Cambridge, MA 02138 Tel: 617-496-7134 Fax: 617-495-2196 email: yfleung@cgr.harvard.edu; yfleung@genomicshome.com URL: http://genomicshome.com

Dear Fai, > Is the FDR assumed to be a certain percent (e.g. 5%) in the FDR adjustment > for p values? No, it is not. When you use multtest you get "adjusted p-values", and thus is up to you to choose the cutting point. The meaning of the "adjusted p-value" is very well explained in the documentation for multtest (look at "multtest.intro"). > p-values the same as/similar to q-values in SAM procedure? They are related, but are not the same. You can look, for example, at the recent paper by Storey and Tibshirani (PNAS, 2003, 100(16): 9440-9445) for explanation of q-values and relation to FDR. Best, Ram?n > > Thanks in advance! > > Best regards, > Fai > ________ > Yuk Fai Leung > Bauer Center for Genomics Research > Harvard University > 7 Divinity Avenue > Cambridge, MA 02138 > Tel: 617-496-7134 > Fax: 617-495-2196 > email: yfleung@cgr.harvard.edu; yfleung@genomicshome.com > URL: http://genomicshome.com > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- Ram?n D?az-Uriarte Bioinformatics Unit Centro Nacional de Investigaciones Oncol?gicas (CNIO) (Spanish National Cancer Center) Melchor Fern?ndez Almagro, 3 28029 Madrid (Spain) Fax: +-34-91-224-6972 Phone: +-34-91-224-6900 http://bioinfo.cnio.es/~rdiaz