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Old 01-27-2014, 08:55 AM   #12
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Originally Posted by polsum View Post

I was wondering if any one can answer my question about FDR

How exactly we should determine the cutoff limit for FDR value? Is 0.1 acceptable or 0.2? Because the number of significantly expressed genes changes dramatically even for slightest changes in FDR value. For a Publication, how much FDR is a good FDR?

If I select P.value < 0.05 and ignore FDR, I am getting around 200 differentially expressed genes. But If I use FDR <0.085 along with P value <0.05, the number drops to 65. can we publish without FDR?

Thanks in advance.
I don't think FDR is very important for RNA-seq. For multiple hypothesis tests where each test has uniform variance and is sufficiently powered, FDR might be OK, however for the counts data FDR doesn't take into account the fact that many of the tests were negative due to insufficient coverage rather than the tests not being discernible, so FDR is confounded by the sampling methodology. IE if you had sampled 1000 genes, and the null hypothesis was rejected for 50, and of the other 950, 80% had low coverage. In theory you could sequence more from the same samples then some of the other 80% could be significant, which doesn't make sense from an FDR stand point. I think this also applies to Bonferroni. On the flip side, you could get a fabulous FDR, by simply not sequencing very much.
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