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In many multiple testing applications in genetics, the signs of the test statistics provide useful directional information, such as whether genes are potentially up‐ or down‐regulated between two experimental conditions. However, most existing procedures that control the false discovery rate (FDR) are P‐value based and ignore such directional information. We introduce a novel procedure, the signed‐knockoff...
Large‐scale homogeneous discrete p‐values are encountered frequently in high‐throughput genomics studies, and the related multiple testing problems become challenging because most existing methods for the false discovery rate (FDR) assume continuous p‐values. In this article, we study the estimation of the null proportion and FDR for discrete p‐values with common support. In the finite sample setting,...
Summary. Many methods for estimation or control of the false discovery rate (FDR) can be improved by incorporating information about π0, the proportion of all tested null hypotheses that are true. Estimates of π0 are often based on the number of p‐values that exceed a threshold λ. We first give a finite sample proof for conservative point estimation of the FDR when the λ‐parameter is fixed. Then...
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