EdgeR: paired samples together with independant samples
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Guest User ★ 13k
@guest-user-4897
Last seen 9.5 years ago
Hello, I am using EdgeR to analyse my RNAseq data. I have: cells from 3 healthy patients , either treated or not with a hormone . cells from 3 patients with disease D1, either treated or not with the hormone cells from 3 patients with disease D2, either treated or not with the hormone. I would like to know what is wrong in the response to the hormone in patients with disease D1 and D2. I don't know how to combine paired comparisons, with pairwise comparisons, in a unique glm analysis. thank you very much, anna -- output of sessionInfo(): R version 2.15.1 (2012-06-22) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252 [3] LC_MONETARY=French_France.1252 LC_NUMERIC=C [5] LC_TIME=French_France.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.15.1 -- Sent via the guest posting facility at bioconductor.org.
RNASeq edgeR RNASeq edgeR • 1.1k views
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@gordon-smyth
Last seen 32 minutes ago
WEHI, Melbourne, Australia
Dear Anna, You are right to recognise that the analysis of this sort of design is more complex than many other experiments, because it includes comparisons both within and between patients. I have included a new section in the edgeR User's Guide based on your experiment that describes the analysis. This will appear in the official release of edgeR in a couple of days. In the meantime, see pages 31-33 of: http://bioinf.wehi.edu.au/software/edgeR/edgeRUsersGuide.pdf Best wishes Gordon > Date: Tue, 23 Oct 2012 06:37:44 -0700 (PDT) > From: "anna [guest]" <guest at="" bioconductor.org=""> > To: bioconductor at r-project.org, m.nadira at yahoo.fr > Subject: [BioC] EdgeR: paired samples together with independant > samples > > > Hello, > I am using EdgeR to analyse my RNAseq data. > > I have: > > cells from 3 healthy patients , either treated or not with a hormone . > > cells from 3 patients with disease D1, either treated or not with the > hormone > > cells from 3 patients with disease D2, either treated or not with the > hormone. > > I would like to know what is wrong in the response to the hormone in > patients with disease D1 and D2. > > I don't know how to combine paired comparisons, with pairwise > comparisons, in a unique glm analysis. > > thank you very much, > anna > > -- output of sessionInfo(): > > R version 2.15.1 (2012-06-22) > Platform: i386-pc-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252 > [3] LC_MONETARY=French_France.1252 LC_NUMERIC=C > [5] LC_TIME=French_France.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > loaded via a namespace (and not attached): > [1] tools_2.15.1 > ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}
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