Hi, I notice in the DESeq vignette<http: bioconductor.org="" packages="" releas="" e="" bioc="" vignettes="" deseq="" inst="" doc="" deseq.pdf=""> there is a "Fixme" comment about including how to test specific comparisons using nbinomGLMTest (page 12). It would be great if someone with experience doing this could let me know how it is done. Thanks in advance, Jamie [[alternative HTML version deleted]]

Hi, On Tue, Nov 26, 2013 at 8:21 AM, James Floyd <j.a.floyd at="" qmul.ac.uk=""> wrote: > Hi, > > I notice in the DESeq vignette<http: bioconductor.org="" packages="" rele="" ase="" bioc="" vignettes="" deseq="" inst="" doc="" deseq.pdf=""> there is a "Fixme" comment about including how to test specific comparisons using nbinomGLMTest (page 12). It would be great if someone with experience doing this could let me know how it is done. Can you be more specific of what you'd like to test? Perhaps you can setup your problem for us and point out what particular comparison you'd like to make, and someone can help you better. Furthermore, if you are using DESeq, you might consider shifting over to DESeq2. It offers a number of benefits over DESeq, and (I believe) this is where the DESeq authors are focussing the lion's share of their attention anyhow. -steve -- Steve Lianoglou Computational Biologist Genentech