Dear all, I am doing DGE multifactorial analysis with EdgeR but I have a problem with somes locus I obtained a large logFC value , perhaps because any comparision there is some zero. Is this possible? or maybe I have some error Thank for your help, waiting your response. Regards, This is the scrip that I am using: d.all<- readDGE(counts.all, skip = 5, comment.char = "!") colnames(d.all$counts)<-counts.all[,3] cpmd.all<-cpm(d.all) d.all <- d.all[rowSums(cpmd.all > 1) >= 2, ] d.all<- calcNormFactors(d.all) designall<-model.matrix(~time+time:d.all$samples$group) d.all <- estimateGLMCommonDisp(d.all, designall) glmfit.all <- glmFit(d.all, designall,dispersion = d.all$common.dispersion) lrt.all <- glmLRT(d.all, glmfit.all, coef=4) topTags(lrt.all,sort.by = "logFC") logConc logFC LR P.Value FDR AT1G22220 -12.30768 -144269488 62.70746 2.398056e-15 2.995171e-12 AT1G08430 -13.45102 -144269487 37.11160 1.115581e-09 2.960891e-07 AT4G11180 -13.84678 144269487 38.22337 6.309211e-10 1.835116e-07 AT5G41880 -13.36909 -144269486 33.88640 5.842556e-09 1.255052e-06 AT1G04610 -13.41465 -144269486 33.44700 7.323248e-09 1.480900e-06 AT2G24850 -14.18267 -144269486 25.85859 3.673666e-07 3.979742e-05 AT5G44635 -13.98784 -144269486 24.61663 6.994557e-07 6.736796e-05 AT1G35690 -13.60305 144269486 27.92875 1.258656e-07 1.590776e-05 AT1G67328 -13.27975 -144269486 24.43246 7.696091e-07 7.262716e-05 AT1G51460 -13.77582 -144269486 24.12274 9.038647e-07 8.123359e-05 sessionInfo() R version 2.14.1 (2011-12-22) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] edgeR_2.5.5 limma_3.10.3 loaded via a namespace (and not attached): [1] tools_2.14.1 Sandra Isabel Gonzalez Morales Graduet Student PhD Centro de Investigacion y de Estudios Avanzados del I.P.N Laboratorio Nacional deGenomica para la Biodiversidad Km. 9.6 Libramiento Norte Carretera Irapuato-Leon Irapuato, Gto. M?xico -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

de.com <- exactTest(d) de<-decideTestsDGEde.com,p.value=0.05) detags<-rownames(d)[as.logical(de)] plotSmearde.com, de.tags=detags) Error in log2(x) : Non-numeric argument to mathematical function I think I followed the user's guide, but still... [[alternative HTML version deleted]]