[BioC] limma 2x2 factorial experiment with two colour arrays, no common reference

[Martin Kerick]

Dear All,

I have a question concerning the "design" of a design matrix.
I don't use Affymetrix arrays and I don't use a common reference.
My experiment is supposed to be a 2x2 factorial experiment with 2
phenotypes(control cells & patient cells) and 2 treatments(treatment &
control(=no treatment)). I would like to know more about the effect of
a) the treatment
b) phenotype patient cells
c) interaction of phenotype patient cells and the treatment (in other words:
what kind of additional effect has my treatment if the phenotype is patient
cells)
on the gene expression in the cells.

I conducted the following experiments:

patient cells/control  vs.  patient cells/treatment	5 independent samples in
dye swap

and

control cells/control  vs.  control cells/treatment    5 independent samples
in dye swap

Questions:

Is it possible to get the effect (a,b,c) out of the experiments with the
help of limma?

If not, what kind of additional experiments do you propose ?
(maybe some cross swaps like patient cells/control vs. control
cells/treatment ?)

How do I use model.matrix especially with regard to the dye swap replicates
?
(I know there are several examples in the manual and in the mailing list,
but none for 2x2 w/o Affy and w/o common ref)

Any help would be greatly appreciated,
regards,

Martin