Yes, I've made the transition to DESeq2 - thanks for the reply. Jamie On 10/01/2014 17:18, "Ryan C. Thompson" <rct at="" thompsonclan.org=""> wrote: >In general, you would subset the CountDataSet to only include the >samples from the two conditions you care about. Do this after >estimating dispersions and before fitNbinomGLMs. > >But more generally, I agree that the real solution is "use DESeq2". > >-Ryan > >On Thu 09 Jan 2014 03:41:39 AM PST, James Floyd wrote: >> Hi, >> >> Thanks for your reply, and sorry for the delay. As always, I got >> distracted by other projects ? >> >> I am looking to perform a DE analysis for a disease with three states, >> while correcting for smoking status. So I was using ? : >> >> fit0 = fitNbinomGLMs( cdsFull, count ~ smoking ) >> fit1 = fitNbinomGLMs( cdsFull, count ~ smoking + condition ) >> >> ? then comparing the models to see whether adding condition improves the >> fit of the model and has a significant effect (as described in the >> vignette). >> >> >> However, if I wanted to make a specific comparison of, say, the two most >> extreme disease states (state A against C, ignoring B), how would I go >> about doing this? >> >> Thanks for letting me know about DESeq2, I was unaware of it. >> >> Cheers, >> Jamie >> >> >> >> On 27/11/2013 17:21, "Steve Lianoglou" <lianoglou.steve at="" gene.com=""> wrote: >> >>> 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="" release="" bioc="" vignettes="" d="" eseq="">>>>in >>>> st/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 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >>http://news.gmane.org/gmane.science.biology.informatics.conductor