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Bioinformatics Advance Access originally published online on October 12, 2004
Bioinformatics 2005 21(5):660-668; doi:10.1093/bioinformatics/bti063
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

A simple procedure for estimating the false discovery rate

Cyril Dalmasso , Philippe Broët * and Thierry Moreau

INSERM U472, Faculté de Médecine Paris-Sud 16 Avenue Paul Vaillant-Couturier, 94807 Villejuif Cedex, France

*To whom correspondence should be addressed.

Motivation: The most used criterion in microarray data analysis is nowadays the false discovery rate (FDR). In the framework of estimating procedures based on the marginal distribution of the P-values without any assumption on gene expression changes, estimators of the FDR are necessarily conservatively biased. Indeed, only an upper bound estimate can be obtained for the key quantity {pi}0, which is the probability for a gene to be unmodified. In this paper, we propose a novel family of estimators for {pi}0 that allows the calculation of FDR.

Results: The very simple method for estimating {pi}0 called LBE (Location Based Estimator) is presented together with results on its variability. Simulation results indicate that the proposed estimator performs well in finite sample and has the best mean square error in most of the cases as compared with the procedures QVALUE, BUM and SPLOSH. The different procedures are then applied to real datasets.

Availability: The R function LBE is available at http://ifr69.vjf.inserm.fr/lbe

Contact: broet{at}vjf.inserm.fr


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