The "Window t-test": a simple and powerful approach to detect differentially expressed genes in microarray datasets

Fabrice Berger, Benoit De Hertogh, Michael Pierre, Anthoula Gaigneaux, Eric Depiereux

Research output: Contribution to journalArticle

Abstract

This work focuses on differential expression analysis of microarray datasets. One way to improve such statistical analyses is to integrate biological information in the design of these analyses. In this paper, we will use the relationship between the level of gene expression and variability. Using this biological information, we propose to integrate the information from multiple genes to get a better estimate of individual gene variance, when a small number of replicates are available, to increase the power of the statistical analysis. We describe a strategy named the "Window t test" that uses multiple genes which share a similar expression level to compute the variance which is then incorporated a classic t test. The performances of this new method are evaluated by comparison with classic and widely- used methods for differential expression analysis (the classic Student t test, the Regularized t test (reg t test), SAM, Limma, LPE and Shrinkage t). In each case tested, the results obtained were at least equivalent to the best performing method and, in most cases, outperformed it. Moreover, the Window t test relies on a very simple procedure requiring small computing power compared with other methods designed for microarray differential expression analysis.
Original languageEnglish
Pages (from-to)327-344
Number of pages18
JournalCentral European Journal of Biology
Volume3
Issue number3
Publication statusPublished - 2008

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Microarrays
Genes
Gene expression
Statistical methods
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Keywords

  • Differential expression Microarray Affymetrix Variance Window t test SAM Regularized t test LPE Limma Shrinkage t

Cite this

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The "Window t-test": a simple and powerful approach to detect differentially expressed genes in microarray datasets. / Berger, Fabrice; De Hertogh, Benoit; Pierre, Michael; Gaigneaux, Anthoula; Depiereux, Eric.

In: Central European Journal of Biology , Vol. 3, No. 3, 2008, p. 327-344.

Research output: Contribution to journalArticle

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