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BMC Bioinformatics. 2014 Jan 15;15:14. doi: 10.1186/1471-2105-15-14.

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

Author information

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

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.

PMID:
24423217
PMCID:
PMC3899927
DOI:
10.1186/1471-2105-15-14
[Indexed for MEDLINE]
Free PMC Article

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