Robust estimation of the false discovery rate.

Bioinformatics 2006 Aug 15;22(16):1979-87. Epub 2006 Jun 15.

Department of Biostatistics, St. Jude Children's Research Hospital 332 N. Lauderdale Street, Memphis, TN 38135, USA.

Motivation: Presently available methods that use p-values to estimate or control the false discovery rate (FDR) implicitly assume that p-values are continuously distributed and based on two-sided tests. Therefore, it is difficult to reliably estimate the FDR when p-values are discrete or based on one-sided tests.

Results: A simple and robust method to estimate the FDR is proposed. The proposed method does not rely on implicit assumptions that tests are two-sided or yield continuously distributed p-values. The proposed method is proven to be conservative and have desirable large-sample properties. In addition, the proposed method was among the best performers across a series of 'real data simulations' comparing the performance of five currently available methods.

Availability: Libraries of S-plus and R routines to implement the method are freely available from www.stjuderesearch.org/depts/biostats.

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http://dx.doi.org/10.1093/bioinformatics/btl328DOI Listing
August 2006
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