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Old 04-27-2016, 05:29 AM   #2
dpryan
Devon Ryan
 
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480
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Your wording is a little confused so it's hard to tell exactly what you're doing in method (1) and (2). How about you just tell us the biological question you want to answer and then one of us can then just tell you the simplest way to do it.

In general, you can get the same answer treating each condition:genotype combination as a separate group and doing comparisons as if you use a more classical factorial design (e.g., "~condition*genotype"). Some questions are simpler to answer with one design vs. the other.

I would strongly encourage you not to do multiple comparisons and then take the intersection of the results. You're absolutely killing your statistical power when you're doing that. You also then lack a fold-change or p-value, which you kind of need to both publishing and follow-up experiments.
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