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

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 webcite.

SUBMITTER: Love MI

PROVIDER: S-EPMC4302049 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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

Love Michael I MI Huber Wolfgang W Anders Simon S

Genome biology 20140101 12

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 interpret ...[more]

PMID: 25516281

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