[BioC] Help to analyse a complex experiment

[Marcelo Luiz de Laia]

Dear Bioconductor users and developers!

We have a complex experiment (for me) and we would like to receive 
suggestions on how to analyse it, if possible.

The design is:

 Var A           Var B        Var C         Var D
-------------      -------------     -------------     -------------
T1     T2      T1     T2    T1     T2     T1     T2

Vars A and C are resistant and Vars B and D are susceptible to T1. T2 is 
a controll.

We are interested to get the data from Vars, treatments (T1 and T2) and 
their interactions effects

I do an analysis using limma for each Vars, but, I dont have an ideia 
how I do an analyse for all.

I appreciate any comentary and/or papers suggestions.

The data set are in a matrix after normalization with vsn package.

Thank you

-- 
Marcelo Luiz de Laia
Ph.D Student in Genetics and Plant Breeding
São Paulo State University (http://www.unesp.br/eng/)
School of Agricultural and Veterinary Sciences
Department of  Technology
Via de Acesso Prof.Paulo Donato Castellane s/n
14884-900   Jaboticabal - SP - Brazil
Fone: +55-016-3209-2675