Limma analysis

Linear models for microarray analysis

Linear models for microarray analysis (Limma) is a R and Bioconductor package for organising and analysing cDNA and Affymetrix microarray data. It is written by Gordon Smyth at WEHI.

Algorithm details

For a p * n matrix of expression intensities, Limma is fitting p linear models (one for each row). The lmFit function does this by calling functions such as lm.series which use lm.fit in Package:Stats. For cDNA/oligo two spotted technologies the matrix of expression intensities is usually the marix M values with respect to treatments. For Affymetrix single channel arrays the expression intensities are directly analysed comparing two treatments.

The linear model reduces to effectively estimating average M values using a categorical design matrix. If correlation between rows (spots) is estimated, then the function duplicateCorrelation is called. This fits a reml model on all genes to estimate a rho correlation matrix. A fisher transformation (identical to atanh(x)) is then applied to the rho matrix and an average rho calculating an mean correlation with trim=0.15 by default, which is then backtransformed to give a consensus correlation.