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Old 01-21-2015, 03:39 PM   #1
Location: Boston

Join Date: Oct 2009
Posts: 65
Default 4 conditions in DESeq2

I have four conditions A, B, C, and D that each have three HTSeq count files.

I want to use DESeq2 to compare A to B, A to C, A to D, B to C, B to D etc.

With DESeq, I would bring all the 12 files into a countDataSet and then I could specify which of the conditions to compare.

With DESeq2, I can bring all the 12 files into a DESeqDataSet, but I can not figure out how to do specify the particular comparisons.
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