A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis

被引：866

作者：

Dillies, Marie-Agnes ^{[1
]}

Rau, Andrea ^{[1
]}

Aubert, Julie ^{[1
]}

Hennequet-Antier, Christelle ^{[1
]}

Jeanmougin, Marine ^{[1
]}

Servant, Nicolas ^{[1
]}

Keime, Celine ^{[1
]}

Marot, Guillemette ^{[1
]}

Castel, David ^{[1
]}

Estelle, Jordi ^{[1
]}

Guernec, Gregory ^{[1
]}

Jagla, Bernd ^{[1
]}

Jouneau, Luc ^{[1
]}

Laloe, Denis ^{[1
]}

Le Gall, Caroline ^{[1
]}

Schaeffer, Brigitte ^{[1
]}

Le Crom, Stephane ^{[1
]}

Guedj, Mickael ^{[1
]}

Jaffrezic, Florence ^{[1
]}

机构：

[1] Inst Pasteur, F-75724 Paris 15, France

来源：

BRIEFINGS IN BIOINFORMATICS | 2013年 / 14卷 / 06期

关键词：

high-throughput sequencing; RNA-seq; normalization; differential analysis; GENE-EXPRESSION; SEQ DATA; TRANSCRIPTOME; QUANTIFICATION; STRATEGY; REVEALS; MOUSE; ARRAY;

D O I：

10.1093/bib/bbs046

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：671 / 683

页数：13

共 46 条

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