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Old 03-14-2012, 06:41 AM   #2
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Join Date: Jan 2009
Posts: 392

You should use the adjusted p-values. This controls for false positives that you get when making multiple comparisons.

EdgeR uses as its default the Benjamini-Hochberg procedure. This is also the default for other programs like DESeq. Other methods are more conservative. I would just stick with Benjamini-Hochberg.

Last edited by chadn737; 03-14-2012 at 06:46 AM.
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