In response to a number of requests, I have added a new argument to the function makeContrasts() in the the limma package. The new argument will accept a set of contrasts as a character vector, thus facilitating the use of makeContrasts() within other functions and the automatic construction of contrast expressions. For example, x <- c("A-B","C-(A+B)/2") makeContrasts(contrasts=x,levels=c("A","B","C")) The change is in limma 2.7.9 which will be available from CRAN in a couple of days. Gordon https://stat.ethz.ch/pipermail/bioconductor/2005-June/009263.html https://stat.ethz.ch/pipermail/bioconductor/2006-March/012326.html https://www.stat.math.ethz.ch/pipermail/bioconductor/2006-August/01384 4.html