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

Martin Kerick m.kerick at mucosa.de
Mon May 17 22:39:15 CEST 2004

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
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


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


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,


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