Hi, In edgeR I do something like this: lrt<-glmLRT(fit,contrast=c(0,0,0,0,0,0,0,0,-1,1)) topTags(lrt) Coefficient: -1*GroupE:Time96 1*GroupJ:Time96 logFC logCPM LR PValue FDR comp369941_c0_seq1 17.19 9.98 1103.8 4.85e-242 3.05e-237 comp436540_c0_seq6 13.42 3.92 216.0 6.91e-49 2.17e-44 comp438623_c0_seq2 -10.88 5.34 199.7 2.43e-45 5.08e-41 comp437945_c0_seq4 -11.37 4.27 184.9 4.06e-42 6.38e-38 comp437052_c0_seq13 -10.57 6.99 147.1 7.64e-34 9.60e-30 comp434611_c0_seq48 -11.08 3.61 116.7 3.34e-27 3.50e-23 comp423571_c0_seq13 -10.68 2.95 114.3 1.10e-26 9.90e-23 comp419207_c0_seq15 -2.94 6.34 113.6 1.63e-26 1.28e-22 comp430114_c0_seq11 -3.42 6.59 97.3 5.82e-23 3.97e-19 comp432078_c0_seq11 -11.19 4.11 97.2 6.31e-23 3.97e-19 But I would like to extract the, say, 50 top ids or the ids that have an FDR below a certain limit. How do I do that? Best Jahn

Hi Jahn, On Tuesday, January 14, 2014 9:17:56 AM, Jahn Davik wrote: > Hi, > In edgeR I do something like this: > > lrt<-glmLRT(fit,contrast=c(0,0,0,0,0,0,0,0,-1,1)) > topTags(lrt) > > Coefficient: -1*GroupE:Time96 1*GroupJ:Time96 > logFC logCPM LR PValue FDR > comp369941_c0_seq1 17.19 9.98 1103.8 4.85e-242 3.05e-237 > comp436540_c0_seq6 13.42 3.92 216.0 6.91e-49 2.17e-44 > comp438623_c0_seq2 -10.88 5.34 199.7 2.43e-45 5.08e-41 > comp437945_c0_seq4 -11.37 4.27 184.9 4.06e-42 6.38e-38 > comp437052_c0_seq13 -10.57 6.99 147.1 7.64e-34 9.60e-30 > comp434611_c0_seq48 -11.08 3.61 116.7 3.34e-27 3.50e-23 > comp423571_c0_seq13 -10.68 2.95 114.3 1.10e-26 9.90e-23 > comp419207_c0_seq15 -2.94 6.34 113.6 1.63e-26 1.28e-22 > comp430114_c0_seq11 -3.42 6.59 97.3 5.82e-23 3.97e-19 > comp432078_c0_seq11 -11.19 4.11 97.2 6.31e-23 3.97e-19 > > > But I would like to extract the, say, 50 top ids or the ids that have an FDR below a certain limit. How do I do that? Do you want the IDs or the table? Anyway, this is just a subsetting operation that you should be familiar with if you are planning to use R for much of anything. tab <- topTags(lrt, Inf) tab <- tab[tab$FDR < 0.05] tab[1:50,] ids <- row.names(tab)[tab$FDR < 0.05] etc, etc. Best, Jim > > Best > Jahn > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099