title: A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis.
abstract: During the last 3 years, a number of approaches for the normalization of RNA sequencing data have emerged in the literature, differing both in the type of bias adjustment and in the statistical strategy adopted. However, as data continue to accumulate, there has been no clear consensus on the appropriate normalization method to be used or the impact of a chosen method on the downstream analysis. In this work, we focus on a comprehensive comparison of seven recently proposed normalization methods for the differential analysis of RNA-seq data, with an emphasis on the use of varied real and simulated datasets involving different species and experimental designs to represent data characteristics commonly observed in practice. Based on this comparison study, we propose practical recommendations on the appropriate normalization method to be used and its impact on the differential analysis of RNA-seq data.
authors.affiliation: Institut Pasteur, PF2 Plate-forme Transcriptome et Epigénome, 28 rue du Dr Roux, Paris CEDEX 15, F-75724 France. Tel.: +33 (0) 145688651; Fax: +33 (0) 145688406; marie-agnes.dillies@pasteur.fr.
authors.forename: Marie-Agnès
authors.initials: MA
authors.lastname: Dillies
authors.forename: Andrea
authors.initials: A
authors.lastname: Rau
authors.forename: Julie
authors.initials: J
authors.lastname: Aubert
authors.forename: Christelle
authors.initials: C
authors.lastname: Hennequet-Antier
authors.forename: Marine
authors.initials: M
authors.lastname: Jeanmougin
authors.forename: Nicolas
authors.initials: N
authors.lastname: Servant
authors.forename: Céline
authors.initials: C
authors.lastname: Keime
authors.forename: Guillemette
authors.initials: G
authors.lastname: Marot
authors.forename: David
authors.initials: D
authors.lastname: Castel
authors.forename: Jordi
authors.initials: J
authors.lastname: Estelle
authors.forename: Gregory
authors.initials: G
authors.lastname: Guernec
authors.forename: Bernd
authors.initials: B
authors.lastname: Jagla
authors.forename: Luc
authors.initials: L
authors.lastname: Jouneau
authors.forename: Denis
authors.initials: D
authors.lastname: Laloë
authors.forename: Caroline
authors.initials: C
authors.lastname: Le Gall
authors.forename: Brigitte
authors.initials: B
authors.lastname: Schaëffer
authors.forename: Stéphane
authors.initials: S
authors.lastname: Le Crom
authors.forename: Mickaël
authors.initials: M
authors.lastname: Guedj
authors.forename: Florence
authors.initials: F
authors.lastname: Jaffrézic
mesh_terms: D059014:High-Throughput Nucleotide Sequencing / Q000379:methods* / Q000592:standards; D017423:Sequence Analysis, RNA / Q000379:methods* / Q000592:standards