Hello, IS there a way of calculating the s0-Value in the SAM analysis? I did a few tets with my data. Every time I get the result >data.sum ... s0 = 0 Number of permutations: 200 MEAN number of falsely called genes is computed. Delta: 9.3 cutlow: -23.092 cutup: 14.528 p0: 0.312 Significant Genes: 8 Falsely Called Genes: 0 FDR: 0 Genes called significant (using Delta = 9.3): Row d.value stdev rawp q.value R.fold Name 1 4431 26.0 5.92 0 0 1.28e+42 254466_at 2 22511 -23.1 16.13 0 0 0.00e+00 259927_at 3 8199 18.4 5.61 0 0 1.83e+25 249456_at 4 14510 16.8 8.99 0 0 8.94e+40 258067_at 5 8351 16.4 10.68 0 0 3.08e+46 252077_at 6 16295 15.6 4.65 0 0 2.22e+20 263441_at 7 6168 14.9 7.62 0 0 1.35e+22 249015_at 8 22152 14.5 18.78 0 0 Inf 257088_at I can define s0 as i like(in the sam line), but I'm not sure which value to give. THX, Assa -- Assa Yeroslaviz L?tzenerstr. 15 51373 Leverkusen

Hi Assa, the s0 value (s0=0) you get is the optimal value of s0 for your data. If you prefer the original definition of Tusher et al. in which s0 is strictly positive set include.zero=FALSE in sam(...). For more details on the different options of sam(...) with the modified t-test see ?sam.dstat. Best, Holger > --- Urspr?ngliche Nachricht --- > Von: Assa Yeroslaviz <assa.yeroslaviz at="" uni-duesseldorf.de=""> > An: bioconductor at stat.math.ethz.ch > Betreff: [BioC] calculation of s0 (siggenes) > Datum: Fri, 28 Oct 2005 13:40:56 +0200 > > Hello, > > IS there a way of calculating the s0-Value in the SAM analysis? > I did a few tets with my data. Every time I get the result > >data.sum > ... > s0 = 0 > > Number of permutations: 200 > > MEAN number of falsely called genes is computed. > > Delta: 9.3 > cutlow: -23.092 > cutup: 14.528 > p0: 0.312 > Significant Genes: 8 > Falsely Called Genes: 0 > FDR: 0 > > > Genes called significant (using Delta = 9.3): > > Row d.value stdev rawp q.value R.fold Name > 1 4431 26.0 5.92 0 0 1.28e+42 254466_at > 2 22511 -23.1 16.13 0 0 0.00e+00 259927_at > 3 8199 18.4 5.61 0 0 1.83e+25 249456_at > 4 14510 16.8 8.99 0 0 8.94e+40 258067_at > 5 8351 16.4 10.68 0 0 3.08e+46 252077_at > 6 16295 15.6 4.65 0 0 2.22e+20 263441_at > 7 6168 14.9 7.62 0 0 1.35e+22 249015_at > 8 22152 14.5 18.78 0 0 Inf 257088_at > > I can define s0 as i like(in the sam line), but I'm not sure which value > to > give. > > THX, > > Assa > > > -- > Assa Yeroslaviz > L?tzenerstr. 15 > 51373 Leverkusen > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > -- Telefonieren Sie schon oder sparen Sie noch?