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Bioinformatics Advance Access published online on October 12, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti063
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received April 7, 2004
Revised June 23, 2004
Accepted July 24, 2004

Article

A simple procedure for estimating the false discovery rate

Cyril Dalmasso 1, Philippe Broët 1*, and Thierry Moreau 1

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

* To whom correspondence should be addressed.


  Abstract

Motivation: The most used criterion in microarray data analysis is nowadays the false discovery rate (F DR). 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 obtain 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 calculating the 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 cases as compared to 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.


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