Bioinformatics and Computational Biology Solutions Using R and Bioconductor

Part of the series Statistics for Biology and Health pp 397-420

limma: Linear Models for Microarray Data

  • G. K. Smyth

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A survey is given of differential expression analyses using the linear modeling features of the limma package. The chapter starts with the simplest replicated designs and progresses through experiments with two or more groups, direct designs, factorial designs and time course experiments. Experiments with technical as well as biological replication are considered. Empirical Bayes test statistics are explained. The use of quality weights, adaptive background correction and control spots in conjunction with linear modelling is illustrated on the β7 data.