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 [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list Bioc-sig-sequencing@r-project.org https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing