I'm trying to use edgeR to analyse RNA-seq data following the guidance of "edgeR: differential expression analysis of digital gene expression data". I have done exactly as the manual told and when tapping the command "d <- DGEList(counts=d, group=group)", then an error comes as "?????????DGEList(counts = d, group = group) : Length of 'group' must equal number of columns in 'data' " However, length(group) shows that the length of the group is 7, and dim(d) = 37435 7. So I think they two are equal, so why I got this error? Many thanks! -- output of sessionInfo(): R version 2.9.1 (2009-06-26) x86_64-redhat-linux-gnu locale: LC_CTYPE=zh_CN.UTF-8;LC_NUMERIC=C;LC_TIME=zh_CN.UTF-8;LC_COLLATE=zh_CN .UTF-8;LC_MONETARY=C;LC_MESSAGES=zh_CN.UTF-8;LC_PAPER=zh_CN.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=zh_CN.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] edgeR_1.2.4 Biobase_2.4.1 -- Sent via the guest posting facility at bioconductor.org.

Hi Cawendish (?), You are using a *very* old version of edgeR and of R. Nearly 3 years in R/Bioconductor time is quite like an eternity. R 2.15 was just released, so I would consider installing that one. Then, install edgeR with: source("http://bioconductor.org/biocLite.R") biocLite("edgeR") And, then try your commands again. And if you aren't already, be sure to read an updated version of the User's guide: http://www.bioconductor.org/packages/release/bioc/html/edgeR.html Best, Mark On 05.04.2012, at 14:48, aliaselin [guest] wrote: > > I'm trying to use edgeR to analyse RNA-seq data following the guidance of "edgeR: differential expression analysis of digital gene expression data". > I have done exactly as the manual told and when tapping the command "d <- > DGEList(counts=d, group=group)", then an error comes as "?????????DGEList(counts = d, group = group) : > Length of 'group' must equal number of columns in 'data' > " > > However, length(group) shows that the length of the group is 7, and dim(d) = 37435 7. > So I think they two are equal, so why I got this error? > Many thanks! > > -- output of sessionInfo(): > > R version 2.9.1 (2009-06-26) > x86_64-redhat-linux-gnu > > locale: > LC_CTYPE=zh_CN.UTF-8;LC_NUMERIC=C;LC_TIME=zh_CN.UTF-8;LC_COLLATE=zh_ CN.UTF-8;LC_MONETARY=C;LC_MESSAGES=zh_CN.UTF-8;LC_PAPER=zh_CN.UTF-8;LC _NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=zh_CN.UTF-8;LC_IDEN TIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] edgeR_1.2.4 Biobase_2.4.1 > > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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 ---------- Prof. Dr. Mark Robinson Bioinformatics Institute of Molecular Life Sciences University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland v: +41 44 635 4848 f: +41 44 635 6898 e: mark.robinson at imls.uzh.ch o: Y11-J-16 w: http://tiny.cc/mrobin