[R] FDR analyses: minimum number of features

Dupont, William william.dupont at Vanderbilt.Edu
Thu Sep 22 15:05:01 CEST 2005

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:kjetil at acelerate.com] 
Sent: Wednesday, September 21, 2005 9:45 PM
To: Spencer Graves
Cc: Dupont, William; r-help at 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
>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?


> 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
>>R-help at stat.math.ethz.ch mailing list
>>PLEASE do read the posting guide! 


Kjetil Halvorsen.

Peace is the most effective weapon of mass construction.
               --  Mahdi Elmandjra

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