Dear All , I am analyzing the Rna-seq data from one sample. I don't have replicates. I have different cell lines (6) from one sample and I am interested in varying genes among different cell lines within the sample. Ideally, I would be interested to find differentially expressed genes in all 36 possible combinations. I have count data for all cell lines. So whether I should analyze by edgeR or DeGseq? Can I perform exact test/GLM on this sort of data. I am very new to analyze this kind of data and I would appreciate any guidance on this regard. Best Rakhs [[alternative HTML version deleted]]

Is that your real name? On Thu, Sep 8, 2011 at 12:28 PM, rakhs shit <rakhs2011@gmail.com> wrote: > Dear All , > I am analyzing the Rna-seq data from one sample. I don't have replicates. > I > have different cell lines (6) from one sample and I am interested in > varying > genes among different cell lines within the sample. Ideally, I would be > interested to find differentially expressed genes in all 36 possible > combinations. I have count data for all cell lines. So whether I should > analyze by edgeR or DeGseq? Can I perform exact test/GLM on this sort of > data. > I am very new to analyze this kind of data and I would appreciate any > guidance on this regard. > Best > Rakhs > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]

Dear Rakhs, See Section 9 "What to do if you don't have replicates" in the edgeR Users' Guide: http://www.bioconductor.org/packages/2.9/bioc/vignettes/edgeR/inst/doc /edgeRUsersGuide.pdf Best wishes Gordon > Date: Thu, 8 Sep 2011 18:28:19 +0200 > From: rakhs shit <rakhs2011 at="" gmail.com=""> > To: bioconductor at r-project.org > Subject: [BioC] edgeR-DeGseq > > Dear All , > I am analyzing the Rna-seq data from one sample. I don't have replicates. I > have different cell lines (6) from one sample and I am interested in varying > genes among different cell lines within the sample. Ideally, I would be > interested to find differentially expressed genes in all 36 possible > combinations. I have count data for all cell lines. So whether I should > analyze by edgeR or DeGseq? Can I perform exact test/GLM on this sort of > data. > I am very new to analyze this kind of data and I would appreciate any > guidance on this regard. > Best > Rakhs ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}