for future reference, in DESeq2 the base mean involves all samples in the dds object. Hi, It is the same calculation, the mean of normalized counts, with the same size factor calculation. Are you sure you are specifying the same gene? Can you provide the code? Mike On Jul 3, 2014 1:59 AM, "Nofar Chen [guest]" <guest@bioconductor.org> wrote: > Hi, > We recently upgraded to DESeq2, and we are trying to figure out the > differences. We couldn't find an explanation in the documentation regarding > the basemean calculations, they are not the same as in DESeq. For example, > for 2 conditions with all samples with count 0 in a specific gene, we get a > basemean of 0 in DESeq, and a basemean of 0.68586719 in DESeq2. I > understand how the calculation is done in DESeq, but not in DESeq2. Can you > explain please? > Thanks > > > -- output of sessionInfo(): > > none > > -- > Sent via the guest posting facility at bioconductor.org. > [[alternative HTML version deleted]]