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

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@stat.math.ethz.ch [mailto:bioconductor- > bounces@stat.math.ethz.ch] On Behalf Of Auer Michael > Sent: Friday, January 07, 2005 1:06 PM > To: bioconductor@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@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor