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Hi Alex, this is explained in the R news article mentioned in the vignette of siggenes. I, however, will also add an explanation to this to the vignette. False is *not* the number of False Positive, but what Tusher et al. call the number of falsely called genes. The number of False Positive is determined by p0 * False. Best, Holger -------- Original-Nachricht -------- > Datum: Thu, 15 Nov 2007 15:31:43 -0500 > Von: "Alex Tsoi" <tsoi.teen at="" gmail.com=""> > An: bioconductor at stat.math.ethz.ch > Betreff: [BioC] Question on SAM output > Dear all, > > I used the sam analysis from the siggenes package to analyze > differentially > expressed genes, and here is the output: > > Delta p0 False Called FDR > 1 0.1 0.235 3033.95 8740 0.08144 > 2 0.2 0.235 2539.17 8596 0.06930 > 3 0.3 0.235 2108.23 8452 0.05852 > 4 0.4 0.235 1788.62 8342 0.05030 > 5 0.5 0.235 1508.60 8226 0.04303 > 6 0.6 0.235 1261.23 8097 0.03655 > 7 0.7 0.235 1048.82 7964 0.03090 > 8 0.8 0.235 879.58 7828 0.02636 > 9 0.9 0.235 761.43 7719 0.02314 > 10 1.0 0.235 661.70 7580 0.02048 > 11 1.1 0.235 590.24 7476 0.01852 > 12 1.2 0.235 535.54 7407 0.01696 > > > I think I understand the mathematics and computation in SAM, but I am not > quite sure how could I comprehend the results: > The "False" column is supposed to be the false positive identified, and > the > "Called" column is the number of genes called to be significantly > differentially expressed, so the FDR is calculated by using False to divid > Called. > > I understand the False is probably just from the average of the null > distribution, but it still doesn't make sense: > eg. if we look at the data when Delta is equal 0.2, there are arond > 2539.17genes that are false positive, while the number of genes Called > to be > significant is 8596, then how could the FDR rate equals to 0.06930 ? > > Am I understand this in a wrong way, could anyone please show me or direct > me to the right direction ? > > I greatly appreciate for any help or comment. > > Thanks, > Alex- > > -- > Lam C. Tsoi (Alex) > Medical University of South Carolina > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- Ist Ihr Browser Vista-kompatibel? Jetzt die neuesten