> d <- DGEList(counts = d, lib.size = lib_size) > #normalization > dge <- calcNormFactors(d) > rm(d) > > fac=factor(c('c0h','c0h','c0h','c24h','c24h','c24h','t0h','t0h','t0h ','t6h','t6h','t6h','t6h','t12h','t12h','t12h','t12h','t18h','t18h','t 18h','t18h', + 't24h','t24h','t24h','t36h','t36h','t36h','t48h','t48h' ,'t48h','c6h','c12h','c18h','c36h','c48h')) > design = model.matrix(~fac) > colnames(design) <- levels(fac) > > dge <- estimateGLMCommonDisp(dge, design) > dge <- estimateGLMTagwiseDisp(dge, design) > glmfit.dge <- glmFit(dge, design, dispersion=dge$tagwise.dispersion) > aa = makeContrasts("t0h-c0h",levels=design) > lrt.dgh <- glmLRT(dge, glmfit.dge, aa) Error in coef.names[coef] : only 0's may be mixed with negative subscripts > sessionInfo() R version 2.15.1 (2012-06-22) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=Chinese (Simplified)_People's Republic of China.936 [2] LC_CTYPE=Chinese (Simplified)_People's Republic of China.936 [3] LC_MONETARY=Chinese (Simplified)_People's Republic of China.936 [4] LC_NUMERIC=C [5] LC_TIME=Chinese (Simplified)_People's Republic of China.936 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] edgeR_2.6.10 limma_3.12.1 loaded via a namespace (and not attached): [1] tools_2.15.1 -- shan gao Room 231(Dr.Fei lab) Boyce Thompson Institute Cornell University Tower Road, Ithaca, NY 14853-1801 Office phone: 1-607-254-1267(day) Official email:sg839 at cornell.edu Facebook:http://www.facebook.com/profile.php?id=100001986532253

Dear Shan Gao, This is not a bug in edgeR. Rather, your code contains a simple syntax error. Looking at the help page for glmLRT would tell you that the third argument for glmLRT is 'coef' rather than 'contrast'. If you want to enter a contrast, you need glmLRT(dge, glmfit.dge, contrast=aa[,"t0h-c0h"]) There are a number of examples in the edgeR documentation that show you this. If you install edgeR 2.6.12, you will be also be able to use: glmLRT(dge, glmfit.dge, contrast=aa) Best wishes Gordon --------------- original message --------------- [BioC] report a potential bug in edgeR wang peter wng.peter at gmail.com Sun Aug 26 05:17:06 CEST 2012 > d <- DGEList(counts = d, lib.size = lib_size) > #normalization > dge <- calcNormFactors(d) > rm(d) > > fac=factor(c('c0h','c0h','c0h','c24h','c24h','c24h','t0h','t0h','t0h', 't6h','t6h','t6h','t6h','t12h','t12h','t12h','t12h','t18h','t18h','t18 h','t18h', + 't24h','t24h','t24h','t36h','t36h','t36h','t48h','t48h','t48h','c6h',' c12h','c18h','c36h','c48h')) > design = model.matrix(~fac) > colnames(design) <- levels(fac) > > dge <- estimateGLMCommonDisp(dge, design) > dge <- estimateGLMTagwiseDisp(dge, design) > glmfit.dge <- glmFit(dge, design, dispersion=dge$tagwise.dispersion) > aa = makeContrasts("t0h-c0h",levels=design) > lrt.dgh <- glmLRT(dge, glmfit.dge, aa) Error in coef.names[coef] : only 0's may be mixed with negative subscripts > sessionInfo() R version 2.15.1 (2012-06-22) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=Chinese (Simplified)_People's Republic of China.936 [2] LC_CTYPE=Chinese (Simplified)_People's Republic of China.936 [3] LC_MONETARY=Chinese (Simplified)_People's Republic of China.936 [4] LC_NUMERIC=C [5] LC_TIME=Chinese (Simplified)_People's Republic of China.936 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] edgeR_2.6.10 limma_3.12.1 loaded via a namespace (and not attached): [1] tools_2.15.1 -- shan gao Room 231(Dr.Fei lab) Boyce Thompson Institute Cornell University Tower Road, Ithaca, NY 14853-1801 Office phone: 1-607-254-1267(day) Official email:sg839 at cornell.edu Facebook:http://www.facebook.com/profile.php?id=100001986532253 ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}