hi, can someone please explain to me, why is it, that I'm always getting the NULL- value when I try to look fot the significance genes: > data.out SAM Analysis for the Two-Class Unpaired Case Assuming Unequal Variances Delta p0 False Called FDR 1 0.1 0.321 8323.01 14987 0.178 2 2.2 0.321 395.88 5892 0.022 3 4.4 0.321 2.78 628 0.001 4 6.5 0.321 0.09 86 0.000 5 8.6 0.321 0.01 14 0.000 6 10.7 0.321 0.00 5 0.000 7 12.9 0.321 0.00 2 0.000 8 15.0 0.321 0.00 2 0.000 9 17.1 0.321 0.00 1 0.000 10 19.2 0.321 0.00 1 0.000 > data.out.sum <- summary(data.out,10) > data.out.sum SAM Analysis for the Two-Class Unpaired Case Assuming Unequal Variances s0 = 0 Number of permutations: 100 MEAN number of falsely called genes is computed. Delta: 10 cutlow: -23.092 cutup: 15.556 p0: 0.321 Significant Genes: 6 Falsely Called Genes: 0 FDR: 0 Genes called significant (using Delta = 10): Row d.value stdev p.value q.value R.fold Name 1 4431 26.001 5.918 0 0 1.276614e+42 254466_at 2 22511 -23.092 16.129 0 0 0.000000e+00 259927_at 3 8199 18.353 5.608 0 0 1.826403e+25 249456_at 4 14510 16.811 8.989 0 0 8.938649e+40 258067_at 5 8351 16.391 10.682 0 0 3.078096e+46 252077_at 6 16295 15.556 4.648 0 0 2.218854e+20 263441_at now, when I'm try to extract the information, I get: > AE0625419.sum.out$row.sig.genes NULL > AE0625419.sum.out$mat.fdr NULL > AE0625419.sum.out$mat.sig NULL Can anyone please tell me, how can i reach these values? THX Assa -- Assa Yeroslaviz L?tzenerstr. 15 51373 Leverkusen

hi, try to first extract your matrix or other elements, with : mat <- attr(data.out.sum,"mat.sig") and then, access it with : mat$Row Nicolas S. Assa Yeroslaviz wrote: >hi, > >can someone please explain to me, why is it, that I'm always getting the NULL- >value when I try to look fot the significance genes: > > >>data.out >> >> >SAM Analysis for the Two-Class Unpaired Case Assuming Unequal Variances > > Delta p0 False Called FDR >1 0.1 0.321 8323.01 14987 0.178 >2 2.2 0.321 395.88 5892 0.022 >3 4.4 0.321 2.78 628 0.001 >4 6.5 0.321 0.09 86 0.000 >5 8.6 0.321 0.01 14 0.000 >6 10.7 0.321 0.00 5 0.000 >7 12.9 0.321 0.00 2 0.000 >8 15.0 0.321 0.00 2 0.000 >9 17.1 0.321 0.00 1 0.000 >10 19.2 0.321 0.00 1 0.000 > > > >>data.out.sum <- summary(data.out,10) >>data.out.sum >> >> >SAM Analysis for the Two-Class Unpaired Case Assuming Unequal Variances > >s0 = 0 > > Number of permutations: 100 > > MEAN number of falsely called genes is computed. > > Delta: 10 > cutlow: -23.092 > cutup: 15.556 > p0: 0.321 > Significant Genes: 6 > Falsely Called Genes: 0 > FDR: 0 > > >Genes called significant (using Delta = 10): > > Row d.value stdev p.value q.value R.fold Name >1 4431 26.001 5.918 0 0 1.276614e+42 254466_at >2 22511 -23.092 16.129 0 0 0.000000e+00 259927_at >3 8199 18.353 5.608 0 0 1.826403e+25 249456_at >4 14510 16.811 8.989 0 0 8.938649e+40 258067_at >5 8351 16.391 10.682 0 0 3.078096e+46 252077_at >6 16295 15.556 4.648 0 0 2.218854e+20 263441_at > >now, when I'm try to extract the information, I get: > > >>AE0625419.sum.out$row.sig.genes >> >> >NULL > > >>AE0625419.sum.out$mat.fdr >> >> >NULL > > >>AE0625419.sum.out$mat.sig >> >> >NULL > >Can anyone please tell me, how can i reach these values? > >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 > > > > > -- Nicolas Servant Equipe Bioinformatique Institut Curie 26, rue d'Ulm - 75248 Paris Cedex 05 - FRANCE Email: Nicolas.Servant at curie.fr Tel: 01 44 32 42 75