I had the same question this morning - noticed a similar thing, while re-running the analyses with no replicates, those with replicates work OK. Simon Anders has apparently been changing some stuff recently in his functions, so hopefully he can explain us, unless we missed an important update... switching the method did not help... Cheers, Michal On 1/27/12 1:27 PM, "Iain Gallagher" <iaingallagher at="" btopenworld.com=""> wrote: > > >Hello List > >I have a question about the use of DESeq to analyse RNA-Seq data from >paired samples. > >Briefly my experimental design involves cells from 6 animals either >infected or uninfected. I would like to use DESeq to examine differences >between these groups taking the biological pairing into account. The data >are very variable (I think - I've no experience with RNA-Seq data until >now) with some animals showing very little response and others showing >large movement for a given gene; some animals have low expression of a >given gene while others have large counts.