[BioC] Basemean calculations with DESeq2

[Nofar Chen [guest]]

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


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