Hello all, Was there any additional discussion about investigating contrasts of multifactor designs within DESeq? I saw this thread: http://article.gmane.org/gmane.science.biology.informatics.conductor/4 0048/match=deseq+contrast but no response was posted to the list. I am essentially looking for the same guidance (R syntax within DESeq for contrasts and interactions). Thanks. Joshua Udall [[alternative HTML version deleted]]

Dear Joshua, edgeR does exactly this. It has the ability to fit any designed experiment with any number of factors, and has an easy interface to extract any contrast from such a fit. See page 17 of the edgeR user's guide for a very simple example of the use of a contrast: http://www.bioconductor.org/packages/release/bioc/vignettes/edgeR/inst /doc/edgeRUsersGuide.pdf Best wishes Gordon > Date: Tue, 19 Jun 2012 15:57:44 -0600 > From: Joshua Udall <jaudall at="" gmail.com=""> > To: bioconductor at r-project.org > Subject: [BioC] DESeq and contrasts > > Hello all, > > Was there any additional discussion about investigating contrasts of > multifactor designs within DESeq? I saw this thread: > http://article.gmane.org/gmane.science.biology.informatics.conductor /40048/match=deseq+contrast > > but no response was posted to the list. I am essentially looking for the > same guidance (R syntax within DESeq for contrasts and interactions). > > Thanks. > Joshua Udall ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}