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Old 02-20-2014, 04:13 PM   #4
Michael Love
Senior Member
Location: Boston

Join Date: Jul 2013
Posts: 333

yes. And with the LRT, note that the log2FoldChange and lfcSE columns in the results object give the log2 fold change and standard error of the last level over the first, which is not related to the LRT statistic, p-value or adjusted p-value in the other columns of the results object.

Also, that is a very low adjusted p-value. We usually use a false discovery rate of 10% for examples. The optimal FDR to aim for depends on the cost of follow-up experiments and the cost of missing a true discovery, of course, but 1/10 or 1/20 is often reasonable. For exploratory experiments 1/5 might make sense.

If you meant 1e-5 for a p-value threshold, we recommend to focus on adjusted p-values for building lists, as these are much more interpretable.
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