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Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

2014; BioMed Central; Volume: 15; Issue: 12 Linguagem: Inglês

10.1186/s13059-014-0550-8

1474-760X

Michael I. Love, Wolfgang Huber, Simon Anders,

RNA Research and Splicing

Abstract In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-seq, for evidence of systematic changes across experimental conditions. Small replicate numbers, discreteness, large dynamic range and the presence of outliers require a suitable statistical approach. We present DESeq2 , a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. This enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression. The DESeq2 package is available at http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html .