[BioC] SAM False and FDR

[Wittner, Ben]

Note in your table below that FDR = p0*(false/called).

See description of FDR and pi_0 in, for example,

Schwender, H., Krause, A., and Ickstadt, K. (2003), "Comparison
of the Empirical Bayes and the Significance Analysis of Microarrays,"
Techical Report, University of Dortmund, Dortmund, Germany,
http://www.sfb475.uni-dortmund.de/berichte/tr44-03.pdf

HTH.

-Ben

> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch [mailto:bioconductor-
> bounces at stat.math.ethz.ch] On Behalf Of Auer Michael
> Sent: Friday, January 07, 2005 1:06 PM
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] SAM False and FDR
> 
> I can't find out what the difference between the number of falsly called
> genes and the displayed False Discovery Rate is. Because the FDR does not
> result in the calculation false/called . The total number of genes in the
> example below is 2193. As far as I know the FDR is the number of falsly
> called genes with respect to the number of genes called.
> 
> SAM Analysis for a set of delta:
>    delta    p0   false called   FDR
> 1    0.2 0.622 1108.24   1519 0.454
> 2    0.4 0.622  831.33   1233 0.420
> 3    0.6 0.622  394.20    851 0.288
> 4    0.8 0.622   21.85    101 0.135
> 
> Thanks for your help
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor