Differential analysis of RNA-Seq data at the gene level using the DESeq package

Abstract

A basic task in the analysis of count data from RNA-Seq is the detection of differentially expressed genes. The count data are presented as a table which reports, for each sample, the number of reads that have been assigned to a gene. Analogous analyses also arise for other assay types, such as comparative ChIP-Seq. The package DESeq provides methods to test for differential expression by use of the negative binonial distribution and a shrinkage estimator for the distribution's variance 1 . This vignette explains the use of the package. For an exposition of the statistical method, please see our paper [1] and the additional information in Section 9.