Competition-based control of the false discovery proportion

DOI10.48550/ARXIV.2011.11939MaRDI QIDQ113057arXivFDO

Authors Arya Ebadi, Uri Keich, Dong Luo, Kristen Emery, Yilun He, William Stafford Noble

Publication date 24 November 2020

Published in arXiv

Full work available at URL https://doi.org/10.48550/ARXIV.2011.11939

arXiv classification

stat.APstat.ME

Abstract: Recently, Barber and Cand`es laid the theoretical foundation for a general framework for false discovery rate (FDR) control based on the notion of "knockoffs." A closely related FDR control methodology has long been employed in the analysis of mass spectrometry data, referred to there as "target-decoy competition" (TDC). However, any approach that aims to control the FDR, which is defined as the expected value of the false discovery proportion (FDP), suffers from a problem. Specifically, even when successfully controlling the FDR at level $alpha$, the FDP in the list of discoveries can significantly exceed $alpha$. We offer FDP-SD, a new procedure that rigorously controls the FDP in the competition (knockoff / TDC) setup by guaranteeing that the FDP is bounded by $alpha$ at any desired confidence level. Compared with the just-published general framework of Katsevich and Ramdas, FDP-SD generally delivers more power and often substantially so in simulated as well as real data.

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