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Open Access Highly Accessed Research article

Determination of the differentially expressed genes in microarray experiments using local FDR

J Aubert, A Bar-Hen, J-J Daudin* and S Robin

Author Affiliations

UMR INAPG/INRA/ENGREF 518, 16, rue C. Bernard, 75231 Paris Cedex 05, France

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BMC Bioinformatics 2004, 5:125  doi:10.1186/1471-2105-5-125

Published: 6 September 2004

Abstract

Background

Thousands of genes in a genomewide data set are tested against some null hypothesis, for detecting differentially expressed genes in microarray experiments. The expected proportion of false positive genes in a set of genes, called the False Discovery Rate (FDR), has been proposed to measure the statistical significance of this set. Various procedures exist for controlling the FDR. However the threshold (generally 5%) is arbitrary and a specific measure associated with each gene would be worthwhile.

Results

Using process intensity estimation methods, we define and give estimates of the local FDR, which may be considered as the probability for a gene to be a false positive. After a global assessment rule controlling the false positive error, the local FDR is a valuable guideline for deciding wether a gene is differentially expressed. The interest of the method is illustrated on three well known data sets. A R routine for computing local FDR estimates from p-values is available at http://www.inapg.fr/ens_rech/mathinfo/recherche/mathematique/outil.html webcite.

Conclusions

The local FDR associated with each gene measures the probability that it is a false positive. It gives the opportunity to compute the FDR of any given group of clones (of the same gene) or genes pertaining to the same regulation network or the same chromosomic region.