Changes

*set up design matrix. Use a different integer for each treatment group. The following example is for a contrast between the first seven groups and the last eight groups. For details on other design matrices see chapter 8 of [[http://www.bioconductor.org/packages/2.3/bioc/vignettes/limma/inst/doc/usersguide.pdf limma User Guide]]

<pre>

pData(eset) #to see phenotype annotation data

design <- model.matrix(~(c(1,1,1,1,1,1,1,0,0,0,0,0,0,0,0)),eset) #for four replicates of each treatment group,