Hi Estefania One more thing: since you have no replicates among your samples you might like to read Section 11 of the edgeR Users Guide "What to do if you have no replicates", which has some ideas about how you might go about accounting for biological variability when you cannot estimate it in the usual way.
Best wishes Davis On 10 August 2011 07:35, Mark Robinson <mark.robin...@imls.uzh.ch> wrote: > 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 > -- --------------------------------------------------------------------------- Davis J McCarthy Research Technician Bioinformatics Division Walter and Eliza Hall Institute of Medical Research 1G Royal Parade, Parkville, Vic 3052, Australia dmccar...@wehi.edu.au http://www.wehi.edu.au _______________________________________________ Bioc-sig-sequencing mailing list Bioc-sig-sequencing@r-project.org https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing