QPROT Blog
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QPROT v1.3.1 had a critical bug in the code that led to conservative estimation of FDR. The bug has been fixed and tested in several gold standard datasets.
There is still a possibility that the global FDRs (FDRup and FDRdown column) can be miscalculated due to numerical underflow -- in which case use localFDR (fdr column) for filtering.