Nucleic Acids Res. 2015 Apr 20;43(7):e47. doi: 10.1093/nar/gkv007. Epub 2015 Jan 20.

limma powers differential expression analyses for RNA-sequencing and microarray studies.

Ritchie ME¹, Phipson B², Wu D³, Hu Y⁴, Law CW⁵, Shi W⁶, Smyth GK⁷.

Author information

1: Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia Department of Mathematics and Statistics, The University of Melbourne, Parkville, Victoria 3010, Australia.
2: Murdoch Childrens Research Institute, Royal Children's Hospital, 50 Flemington Road, Parkville, Victoria 3052, Australia.
3: Department of Statistics, Harvard University, 1 Oxford Street, Cambridge, MA 02138-2901, USA.
4: Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia.
5: Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland.
6: Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia Department of Computing and Information Systems, The University of Melbourne, Parkville, Victoria 3010, Australia.
7: Department of Mathematics and Statistics, The University of Melbourne, Parkville, Victoria 3010, Australia Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia smyth@wehi.edu.au.

Abstract

limma is an R/Bioconductor software package that provides an integrated solution for analysing data from gene expression experiments. It contains rich features for handling complex experimental designs and for information borrowing to overcome the problem of small sample sizes. Over the past decade, limma has been a popular choice for gene discovery through differential expression analyses of microarray and high-throughput PCR data. The package contains particularly strong facilities for reading, normalizing and exploring such data. Recently, the capabilities of limma have been significantly expanded in two important directions. First, the package can now perform both differential expression and differential splicing analyses of RNA sequencing (RNA-seq) data. All the downstream analysis tools previously restricted to microarray data are now available for RNA-seq as well. These capabilities allow users to analyse both RNA-seq and microarray data with very similar pipelines. Second, the package is now able to go past the traditional gene-wise expression analyses in a variety of ways, analysing expression profiles in terms of co-regulated sets of genes or in terms of higher-order expression signatures. This provides enhanced possibilities for biological interpretation of gene expression differences. This article reviews the philosophy and design of the limma package, summarizing both new and historical features, with an emphasis on recent enhancements and features that have not been previously described.