A leave-p-out based estimation of the proportion of null hypotheses

Abstract

In the multiple testing context, a challenging problem is the estimation of the proportion $π_0$ of true-null hypotheses. A large number of estimators of this quantity rely on identifiability assumptions that either appear to be violated on real data, or may be at least relaxed. Under independence, we propose an estimator $\hatπ_0$ based on density estimation using both histograms and cross-validation. Due to the strong connection between the false discovery rate (FDR) and $π_0$, many multiple testing procedures (MTP) designed to control the FDR may be improved by introducing an estimator of $π_0$. We provide an example of such an improvement (plug-in MTP) based on the procedure of Benjamini and Hochberg. Asymptotic optimality results may be derived for both $\hatπ_0$ and the resulting plug-in procedure. The latter ensures the desired asymptotic control of the FDR, while it is more powerful than the BH-procedure. Finally, we compare our estimator of $π_0$ with other widespread estimators in a wide range of simulations. We obtain better results than other tested methods in terms of mean square error (MSE) of the proposed estimator. Finally, both asymptotic optimality results and the interest in tightly estimating $π_0$ are confirmed (empirically) by results obtained with the plug-in MTP.