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Old 11-17-2015, 04:58 AM   #14
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

1. This isn't actually a pair-wise comparison, it's a classical factorial design (sorry, I know this gets overly confusing...I swear this makes sense if someone just draws stuff on a white board!). For this, you just want the results() from "condition" (using a contrast as you did is nice since then you know whether WT or KO is the numerator).

2. That should work, though you might specify results(dds, name="condition:stimulation") or something like that to be absolutely sure.
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