Hi Gordon, Thanks for the response. One of my data sets has 8 conditions and no replicates and so I wanted to emulate DESeq's way of pooling the samples and also use an offset matrix. I was hoping to avoid doing it manually so that I don't mess it up. I could do this all in edgeR and pool the samples but I'm not sure how well this would work under edgeR vs. DESeq. I am curious though what sounds off to you in my previous email. I don't feel entirely comfortable doing this manually but hopefully it's just because I left out some details. I was trying to follow the DESeq method and the only difference I saw was in the size factor calculations which I changed for my own needs by using the offset values for each tag and sample.
I appreciate the help! Best, Sean On Fri, Jul 15, 2011 at 12:02 AM, Gordon K Smyth <sm...@wehi.edu.au> wrote: > Hi Sean, > > I'm curious to know why not use edgeR, since edgeR does what you want and > DESeq doesn't? > > I might be wrong, but the manual analysis that you describe doesn't sound > right. > > Best wishes > Gordon > > Date: Thu, 14 Jul 2011 12:54:49 -0700 >> From: Sean Ruddy <srudd...@gmail.com> >> To: bioc-sig-sequencing@r-project.**org<bioc-sig-sequencing@r-project.org> >> Subject: [Bioc-sig-seq] Supplying own variance functions and adjusted >> counts to a DESeq dataset >> >> Hi, >> >> I have a RNA-Seq count data set that requires separate offset values for >> each tag and sample. DESeq does not appear to take a matrix of offset >> values >> (unlike edgeR) in any of its functions so I've carried out the analysis >> manually, ie. calculating a size factor for each tag of each sample, >> adjusting the counts, then proceeding to calculate means and variances of >> the adjusted counts, and finally fitting a curve for each condition to the >> mean-var plot using locfit(). >> >> Essentially, I'd like to put these variance functions (or at least all the >> predicted variances) and adjusted counts inside a DESeq object so that I >> can >> take advantage of the other functions DESeq offers, tests, plots, etc... >> >> Thanks for the help! >> >> Sean >> > > ______________________________**______________________________**__________ > The information in this email is confidential and inte...{{dropped:10}} _______________________________________________ Bioc-sig-sequencing mailing list Bioc-sig-sequencing@r-project.org https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing