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

作者：Marie‐Agnès Dillies, Andréa Rau, Julie Aubert, Christelle Hennequet‐Antier, Marine Jeanmougin, Nicolas Servant, Céline Keime, Guillemette Marot, David Castel, Jordi Estellé, Grégory Guernec, Bernd Jagla, Luc Jouneau, Dénis Laloë, Caroline Le Gall, Brigitte Schaeffer, Stéphane Le Crom, Mickaël Guedj, Florence Jaffrézic · 发表于：Briefings in Bioinformatics · 年份：2012 · DOI：10.1093/bib/bbs046 · 被引用次数：1404 · 研究领域：Genomics and Phylogenetic Studies、Gene expression and cancer classification、Molecular Biology Techniques and Applications

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.