I used DESeq2 version 1.4 on some RNSeq data four month ago, and repeat the analysis within version 1.5 last week on the same dataset. I got pretty much the same DE gene lists (>90% overlaps), only the fold changes looked much shrunk from version 1.5. We have some rtPCR data correlated better to the old fold change ranges though. I am aware of you’d changed the beta prior variance estimation. Could you provide more details about it? Thanks a million in advance!