Hi,

We're comparing an older version of DESeq with the new 1.6 version and I'm finding a large discrepancy.  Probably an option I'm missing or something.  In the samples I'm working with, I see total DE genes going from ~200 - 2000 genes at FDR = 0.10 to nearly 0 genes using the new version at the same FDR.

What could be going on here.  Admittedly, the old version was 1.2 so we were way behind but I'm still shocked by this drop off.

Thoughts?

todd

	[[alternative HTML version deleted]]

