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Comparison of normalization methods for differential gene expression analysis in RNA-Seq experiments: A matter of relative size of studied transcriptomes

Maza, Elie and Frasse, Pierre and Senin, Pavel and Bouzayen, Mondher and Zouine, Mohamed Comparison of normalization methods for differential gene expression analysis in RNA-Seq experiments: A matter of relative size of studied transcriptomes. (2013) Communicative & Integrative Biology, 6 (6). e25849. ISSN 1942-0889

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Official URL: http://dx.doi.org/10.4161/cib.25849

Abstract

In recent years, RNA-Seq technologies became a powerful tool for transcriptome studies. However, computational methods dedicated to the analysis of high-throughput sequencing data are yet to be standardized. In particular, it is known that the choice of a normalization procedure leads to a great variability in results of differential gene expression analysis. The present study compares the most widespread normalization procedures and proposes a novel one aiming at removing an inherent bias of studied transcriptomes related to their relative size. Comparisons of the normalization procedures are performed on real and simulated data sets. Real RNA-Seq data sets analyses, performed with all the different normalization methods, show that only 50% of significantly differentially expressed genes are common. This result highlights the influence of the normalization step on the differential expression analysis. Real and simulated data sets analyses give similar results showing 3 different groups of procedures having the same behavior. The group including the novel method named “Median Ratio Normalization” (MR N) gives the lower number of false discoveries. Within this group the MR N method is less sensitive to the modification of parameters related to the relative size of transcriptomes such as the number of down- and upregulated genes and the gene expression levels. The newly proposed MR N method efficiently deals with intrinsic bias resulting from relative size of studied transcriptomes. Validation with real and simulated data sets confirmed that MR N is more consistent and robust than existing methods.

Item Type:Article
Additional Information:Thanks to Landes Bioscience editor. The definitive version is available at http://www.sciencedirect.com The original PDF of the article can be found at Communicative & Integrative Biology website : https://www.landesbioscience.com/journals/cib/
HAL Id:hal-00982548
Audience (journal):International peer-reviewed journal
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Institution:Université de Toulouse > Institut National Polytechnique de Toulouse - Toulouse INP (FRANCE)
French research institutions > Institut National de la Recherche Agronomique - INRA (FRANCE)
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Deposited On:24 Apr 2014 07:48

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