Hi Laura > I have a set of DEG illumina data, coming from 12 different accessions > with replicates of each samples. I have been taking a look at edgeR and > DESeq to analyse the data, and extract differential expressed tags. > However all analysis seem to be based in pair comparasions. Is there any > packge to made comparesions between a greater number of groups? Do you > know if anybody is planning to add this analysis in any existing package? First: Please send such questions to 'bioconductor at r-project.org', not 'bioc-devel at r-project'. The latter is for more internal, technical discussions. Both, edgeR and DESeq, support more general designs using he framework of generalized linear models. See the vignettes for details. If necessary, ask again, describing in more detail what you want to do, and we may be able to help you encoding your design. Simon