Dear List,
I have been trying to use limma to identify differentially expressed genes
but have been finding some difilcuties in creating a basic model.matrix. and
establishing a contrast. I usually have two different types of RNA in
triplicates, a reference an an experimental and wish to see genes
differentially expressed between the them. Following the limma manual my
model.matrix would be:

design <- model.matrix (~ -1 + factor (c (0,0,0,1,1,1)))

Could it be done this way???

In such case, what would be the best way to fit a contrast between my
reference and experimental???

Any help would be greatly appreciated!

best regards,
-- 
Marcos B. Pinho
Programa de Engenharia Química - PEQ
Laboratório de Engenharia de Cultivos Celulares- LECC
Universidade Federal do Rio de Janeiro - UFRJ
Instituto Nacional de Câncer - INCA
Rio de Janeiro - Brasil

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