[R] design

[daniela.marconi@libero.it]

Hi

I have not understood very well how to realize, in limma package, 
the design (using factor in model.matrix) to insert in lmFit.
I have an experiment with 4 groups (a,b,c,d) with 3 replicates for each-one
and i have to compare a vs b; c vs d; ( a&c )vs (b&d).
List Sample in pdata is like this: 
1a
1c
1b
1d
2a
2c
2b
2d
3a
3c
3b
3d
How can i do this design with matrix model?
thanks 
daniela