Hi Estefania, In your $samples data.frame, you don't have a "group" variable listed (it doesn't recognize "files"). Perhaps you made this yourself instead of using the DGEList() constructor?
You could reconstruct this with: RG1 <- DGEList(counts=RG$counts, group=c("allcontrol","allstress")) d <- estimateCommonDisp(RG) Hope that helps, Mark On Aug 10, 2011, at 5:51 AM, Estefania Mancini wrote: > Dear All > I am trying to analyse 2 454 RNA-seq dataset. > I have only 2 condition, control and stress- > It is possible to use edgeR? I have prepared the file with the columns > tags->reads. > I can load the files and build the "object of class "DGEList", which looks > like this: > >> RG > An object of class "DGEList" > $samples > files lib.size norm.factors > allcontrol allcontrol.txt 318020 1 > allstress allstress.txt 306479 1 > > $counts > allcontrol allstress > Gen11900.1 50872 51431 > Gen12050.1 39874 40052 > Gen24780.1 33951 32149 > Gen12070.1 26733 29256 > Gen11930.1 23858 28396 > 18213 more rows ... > > but when I try to apply: >> d = estimateCommonDisp(RG) > I have the following error: > Error in `$<-.data.frame`(`*tmp*`, "group", value = integer(0)) : > replacement has 0 rows, data has 2 > > So I cannot continue analysing the data. > Any suggestion will be helpful > Thanks in advance > Estefania > > _______________________________________________ > Bioc-sig-sequencing mailing list > Bioc-sig-sequencing@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing _______________________________________________ Bioc-sig-sequencing mailing list Bioc-sig-sequencing@r-project.org https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing