For users of limma, the edgeR package has a number of analogous functions. Once the data have been processed and the dispersion estimates are moderated, the topTags function can be used to tabulate the top differentially expressed genes (or tags or exons, etc.). Also, MA (log ratio versus abundance) plots can be created using the plotSmear function, allowing the same visualizations for DGE data as used for microarray data analysis (Fig. 1).
