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limma | Use of within-array replicate spots for assessing differential expression in microarray experiments


Provides an integrated solution for analysing data from gene expression experiments. limma contains rich features for handling complex experimental designs and for information borrowing to overcome the problem of small sample sizes. It also contains particularly strong facilities for reading, normalizing and exploring such data. Recently, the capabilities of limma have been significantly expanded in two important directions: (i) it can perform both differential expression and differential splicing analyses of RNA-seq data; (ii) 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.

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limma is a tool for reading, pre-processing, manipulate, quality control and analyse microarray data from a variety of different technologies. In my opinion, it could easily be considered the state-of-the-art tool for analysis of these kind of data. Linear modelling extended by limma provides a powerful way to analyse simple or complex experiments, allowing full control over covariates and time-series designs. Also, the team behind the tool made great effort in creating a tool easily accessible to non bio-statisticians, which is a plus in a lot of ways. Besides, I should also point out that limma has the capability to analyse RNA-seq experiments as well. Finally, users should definitely check the comprehensive (and well-written) limma User Guide, a document that will provide all the basics to get things rolling with the package.

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limma classification

limma specifications

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GNU General Public License version 2.0
Linear Models for Microarray Data
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  • Gordon Smyth <>


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Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia

Funding source(s)

National Health and Medical Research Council Project Grant [1050661 and 1023454]; NHMRC Program Grant [1054618]; Victorian State Government Operational Infrastructure Support and Australian Government NHMRC IRIISS

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