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Old 09-16-2015, 08:25 AM   #5
dpryan
Devon Ryan
 
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480
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Ah, I had missed that you explicitly requested an LRT with DESeq(). The default is Wald there too. The models that you're testing are completely different between the two methods. With a Wald test, you can test individual coefficient, with the LRT you're testing a more generic interaction.

Edit: Yes, an LRT is likely what you want, since it asks the question, "what genes generally interact in a time:condition dependent manner, regardless of the exact time point".

Last edited by dpryan; 09-16-2015 at 08:39 AM.
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