This note describes the software package edgeR (empirical analysis of DGE in R), which forms part of the Bioconductor project (Gentleman et al., 2004). edgeR is designed for the analysis of replicated count-based expression data and is an implementation of methology developed by Robinson and Smyth (2007, 2008). Although initially developed for serial analysis of gene expression (SAGE), the methods and software should be equally applicable to emerging technologies such as RNA-seq (Li et al., 2008; Marioni et al., 2008) giving rise to digital expression data. edgeR may also be useful in other experiments that generate counts, such as ChIP-seq, in proteomics experiments where spectral counts are used to summarize the peptide abundance (Wong et al., 2008), or in barcoding experiments where several species are counted (Andersson et al., 2008). The software is designed for finding changes between two or more groups when at least one of the groups has replicated measurements.
