Re: [R] FDR analyses: minimum number of features
Thanks. That is an excellent idea. Bill -Original Message- From: Spencer Graves [mailto:[EMAIL PROTECTED] Sent: Thursday, September 22, 2005 9:01 PM To: Dupont, William Cc: Kjetil Brinchmann Halvorsen; r-help@stat.math.ethz.ch Subject: Re: [R] FDR analyses: minimum number of features Have you considered Monte Carlo? From previous work, you could estimate a distribution for the differences to be detected and use that as input to a Monte Carlo, computing thereby a distribution for FDR as a function of distribution of differences and the number of features. From this, you could estimate probabilities for obtaining results that were bogus vs. marginal, barely useful vs. highly accurate and plot them vs. alternative budgets, etc. I hope this comment makes more sense than my earlier nonsense. spencer graves __ 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
[R] FW: FDR analyses: minimum number of features
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
Re: [R] FDR analyses: minimum number of features
I agree. What is unclear to me is the optimal way of justifying sample size and SNP selection in grant applications that use the FDR approach. -Original Message- From: Kjetil Brinchmann Halvorsen [mailto:[EMAIL PROTECTED] Sent: Wednesday, September 21, 2005 9:45 PM To: Spencer Graves Cc: Dupont, William; r-help@stat.math.ethz.ch Subject: Re: [R] FDR analyses: minimum number of features Spencer Graves wrote: Two thoughts on this: 1. Your FDR (Not Franklin Delano Roosevelt) sounds like another name for Type I error rate. It is certainly not the same as type I error rate. Type I error rate is the proportion of true nulls which are rejected, while the FDR is the proportion of rejected null hypothesis which really are true nulls! To me FDR seems like a more promising avenue to multiple testing than the old familywise error rate. Who knows what is a family? Kjetil 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 -- Kjetil Halvorsen. Peace is the most effective weapon of mass construction. -- Mahdi Elmandjra -- No virus found in this outgoing message. Checked by AVG Anti-Virus. 20/09/2005 __ 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
[R] FDR analyses: minimum number of features
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
