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In papyro comparison of TMM (edgeR), RLE (DESeq2), and MRN normalization methods for a simple two-conditions-without-replicates RNA-Seq experimental design

Maza, Elie In papyro comparison of TMM (edgeR), RLE (DESeq2), and MRN normalization methods for a simple two-conditions-without-replicates RNA-Seq experimental design. (2016) Frontiers in Genetics, 7 (164). ISSN 1664-8021

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Official URL: http://dx.doi.org/10.3389/fgene.2016.00164

Abstract

In the past 5 years, RNA-Seq has become a powerful tool in transcriptome analysis even though computational methods dedicated to the analysis of high-throughput sequencing data are yet to be standardized. It is, however, now commonly accepted that the choice of a normalization procedure is an important step in such a process, for example in differential gene expression analysis. The present article highlights the similarities between three normalization methods: TMM from edgeR R package, RLE from DESeq2 R package, and MRN. Both TMM and DESeq2 are widely used for differential gene expression analysis. This paper introduces properties that show when these three methods will give exactly the same results. These properties are proven mathematically and illustrated by performing in silico calculations on a given RNA-Seq data set.

Item Type:Article
Additional Information:Thanks to Frontiers Media editor. The definitive version is available at http://journal.frontiersin.org/article/10.3389/fgene.2016.00164/full
HAL Id:hal-01494988
Audience (journal):International peer-reviewed journal
Uncontrolled Keywords:
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 Mar 2017 11:59

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