[BioC] additional info on limma models and contrasts

[Susan Huse]

Hi, 

I am using limma for a variety of projects. It all seems pretty straightforward for projects where I am not as concerned with the interaction of the independent variables, 
but I am a bit confused on how to create the contrasts so that I can focus the analysis on the interactions between the independent variables.  I have read the users' guides and vignettes and the help pages, but haven't found a good explanation for setting up a more complex model.matrix and contrasts and how to make proper use of all the information embedded in the limma object.  Does anyone have a recommendation for a more comprehensive discussion and tutorial?

Thanks in advance, 
Sue Huse