The overly conservative calling of the old DESeq tool can be observed, with reduced sensitivity compared to the other algorithms and an actual FDR less than the nominal value of 0.1. We note that EBSeq version 1.4.0 by default removes low-count genes – whose 75% quantile of normalized counts is less than ten – before calling differential expression. The sensitivity of algorithms on the simulated data across a range of the mean of counts are more closely compared in Additional file 1: Figure S9.
