experiment design in EdgeR
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@guest-user-4897
Last seen 9.5 years ago
Hello, I am using EdgeR to analyse RNAseq data. I would like to know whether I should use several paired analyses or a blocking analysis for this paired experiment: I have cells from3 patients. For each patient, I have 3 conditions: cells were either Non treated, treated with drug 1, or treated with drug 2. I would like to know what each drug does, and the difference between them. I have a doubt because in this case a block would be one patient, so cells are exactly the same. Then I have the same question whether to use several paired analyses, or first a blocking analysis for each group followed by several paired analyses, or another kind of analysis for those paired experiments: 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. 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 -- Sent via the guest posting facility at bioconductor.org.
RNASeq edgeR RNASeq edgeR • 981 views
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@gordon-smyth
Last seen 1 hour ago
WEHI, Melbourne, Australia
Dear Anna, > Date: Tue, 23 Oct 2012 01:27:13 -0700 (PDT) > From: "anna [guest]" <guest at="" bioconductor.org=""> > To: bioconductor at r-project.org, m.nadira at yahoo.fr > Subject: [BioC] experiment design in EdgeR > > > Hello, > I am using EdgeR to analyse RNAseq data. > I would like to know whether I should use several paired analyses or a blocking analysis for this paired experiment: > I have cells from3 patients. For each patient, I have 3 conditions: cells were either Non treated, treated with drug 1, or treated with drug 2. > I would like to know what each drug does, and the difference between them. > I have a doubt because in this case a block would be one patient, so cells are exactly the same. Thsi is a blocked design, described in Section 3.4.2 "Blocking" in the edgeR User's Guide. > Then I have the same question whether to use several paired analyses, or > first a blocking analysis for each group followed by several paired > analyses, or another kind of analysis for those paired experiments: > > 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. Just treat this is six groups, following Section 3.3.31 "Defining each treatment combination as a group" in the edgeR User's Guide. If you can't find these sections in your User's Guide, then update the current Bioconductor release. Best wishes Gordon > I would like to know what is wrong in the response to the hormone in patients with disease D1 and D2. > > 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 ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}
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Dear Anna, I replied to your question below too quickly, and my advice below was too simple. For better advice, see the response I made a few minutes ago to your later posting regarding the same experiment. Best wishes Gordon On Wed, 24 Oct 2012, Gordon K Smyth wrote: > Dear Anna, > >> Date: Tue, 23 Oct 2012 01:27:13 -0700 (PDT) >> From: "anna [guest]" <guest at="" bioconductor.org=""> >> To: bioconductor at r-project.org, m.nadira at yahoo.fr >> Subject: [BioC] experiment design in EdgeR >> >> >> Then I have the same question whether to use several paired analyses, or >> first a blocking analysis for each group followed by several paired >> analyses, or another kind of analysis for those paired experiments: >> >> 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. > > Just treat this is six groups, following Section 3.3.31 "Defining each > treatment combination as a group" in the edgeR User's Guide. > > If you can't find these sections in your User's Guide, then update the > current Bioconductor release. > > Best wishes > Gordon > >> I would like to know what is wrong in the response to the hormone in >> patients with disease D1 and D2. >> >> thank you very much, >> anna ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}
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