Yes, exactly. See the section 'Multi-factor designs' in the vignette of DESeq or DESeq2. Note that for DESeq2, we recommend to put the variable of interest, say 'condition' taking values {normal, tumor} at the end of the design formula, because the results() and plotMA() functions by default will pull from the last variable of the design formula: ~ patient + condition Mike On Fri, Aug 30, 2013 at 8:39 AM, Devon Ryan <dpryan@dpryan.com> wrote: > Hi Prabhakar, > > The general method you're looking for is to add "patient" (or whatever > term you prefer) as a factor in your design. So, if you denote tumor/normal > by a factor called "status": > > counts ~ status + patient > > would likely be the formula you want. You could also allow an interaction > if it makes sense for your dataset, by swapping an asterisk for the plus > sign. You'll need to specify the individual patients in your dataframe, of > course. > > Best, > Devon > > ____________________________________________ > Devon Ryan, Ph.D. > Email: dpryan@dpryan.com > Molecular and Cellular Cognition Lab > German Centre for Neurodegenerative Diseases (DZNE) > Ludwig-Erhard-Allee 2 > 53175 Bonn, Germany > > On Aug 30, 2013, at 12:12 AM, Prabhakar Chalise wrote: > > > Hi, > > > > I was looking for a method to identify differentially expressed genes > using the paired tumor/normal samples. Is there a method under DEseq to > test for such correlated data? > > > > Thanks, > > -Prabhakar Chalise > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]