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Open Access Highly Accessed Research article

Fold change rank ordering statistics: a new method for detecting differentially expressed genes

Doulaye Dembélé12* and Philippe Kastner13

Author Affiliations

1 Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964, CNRS UMR 7104, Université de Strasbourg, 67404 Illkirch, France

2 IGBMC Microarray and Sequencing Platform, 67404 Illkirch, France

3 Faculté de Medécine, Université de Strasbourg, Strasbourg, France

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BMC Bioinformatics 2014, 15:14  doi:10.1186/1471-2105-15-14

Published: 15 January 2014

Abstract

Background

Different methods have been proposed for analyzing differentially expressed (DE) genes in microarray data. Methods based on statistical tests that incorporate expression level variability are used more commonly than those based on fold change (FC). However, FC based results are more reproducible and biologically relevant.

Results

We propose a new method based on fold change rank ordering statistics (FCROS). We exploit the variation in calculated FC levels using combinatorial pairs of biological conditions in the datasets. A statistic is associated with the ranks of the FC values for each gene, and the resulting probability is used to identify the DE genes within an error level. The FCROS method is deterministic, requires a low computational runtime and also solves the problem of multiple tests which usually arises with microarray datasets.

Conclusion

We compared the performance of FCROS with those of other methods using synthetic and real microarray datasets. We found that FCROS is well suited for DE gene identification from noisy datasets when compared with existing FC based methods.

Keywords:
Differentially expressed genes; Fold change; Averages of ranks; Microarray