[R] FDR analyses: minimum number of features

Kjetil Brinchmann Halvorsen kjetil at acelerate.com
Thu Sep 22 04:45:11 CEST 2005

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?


> 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! 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.

More information about the R-help mailing list