cutoff for significant TMP values

horvathdp

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Join Date: Dec 2011

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cutoff for significant TMP values

10-30-2014, 11:59 AM

So what are people using these days as a cutoff for significance with EBseq normalized results? I am using FDR<0.05 and at least 10 TPM for all biological replicates in at least one of my treatment groups. I went that high because I noticed that I had a fair number of non-plant contigs that showed up as significantly differential when I just used the FDR cutoff, and when I required a moderate level of expression, about 90% of those non-plant contigs were removed. I'd like to know what others are using and if there is any reasons underlying the common cutoff criteria.

Thanks!
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