Dear Dr. Graves Many thanks for your response. FDRs and their associated q values do differ from Type I error rates and P values (See Storey and Tibshirani PNAS 2003;100:9440-5). It is an approach that is rapidly gaining popularity in the analysis of genomic data where we have massive numbers of covariates measured on a comparatively modest number of subjects. To my mind it is a real advance in dealing with the extreme multiple comparisons problems that afflict such data. Unfortunately, it is still a relatively new technique and I do not believe that a consensus as to the number of needed response features has been reached.
Submitting my question to the R-help list was a long shot, although Storey's software for this methodology is written in R. With best wishes, Bill Dupont -----Original Message----- From: Spencer Graves [mailto:[EMAIL PROTECTED] Sent: Wednesday, September 21, 2005 9:27 AM To: Dupont, William Cc: r-help@stat.math.ethz.ch Subject: Re: [R] FDR analyses: minimum number of features Two thoughts on this: 1. Your FDR (Not Franklin Delano Roosevelt) sounds like another name for Type I error rate. The definition of "reasonably reliable FDRs" would seem to relate to the status of the literature on this issue among researchers in genotyping. As more reports of FRDs in genotyping are published, I would expect that methodology for estimation and the standard for accuracy would similarly evolve. 2. Have you tried the Bioconductor (www.bioconductor.org/) listserve? They might be able to say something more useful than a general list like this. spencer graves Dupont, William wrote: > Dear List, > > We are planning a genotyping study to be analyzed using false > discovery rates (FDRs) (See Storey and Tibshirani PNAS 2003; > 100:9440-5). I am interested in learning if there is any consensus as > to how many features (ie. how many P values) need to be studied before > reasonably reliable FDRs can be derived. Does anyone know of a > citation where this is discussed? > > Bill Dupont > > William D. Dupont phone: 615-343-4100 URL > http://biostat.mc.vanderbilt.edu/twiki/bin/view/Main/WilliamDupont > > ______________________________________________ > R-help@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! > http://www.R-project.org/posting-guide.html -- Spencer Graves, PhD Senior Development Engineer PDF Solutions, Inc. 333 West San Carlos Street Suite 700 San Jose, CA 95110, USA [EMAIL PROTECTED] www.pdf.com <http://www.pdf.com> Tel: 408-938-4420 Fax: 408-280-7915 ______________________________________________ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html