[BioC] Limma: combining 2 microarray studies

[Ana Conesa]

Hi,
I have been asked to analyze jointly two different microarray studies (2 
color technology). They use the same microarray platform and represent the 
same biological process but each one follows a different experimental design 
and evaluate slightly different conditions
One study has a reference design, while the other is a dye-swap of pairs 
treatment vs. control, schematically
Study A:
	Cy3	Cy5
chipA1  trt1	reference
chipA2  trt1	reference
chipA3  trt2	reference
chipA4  trt2	reference
.....

Study B
	  Cy3		Cy5
chipB1  trt3		control.trt3
chipB2  control.trt3	trt3
chipB3  trt4		control.trt4
chipB4  control.trt3	trt4
.....


We would like to make comparisons between treatments in Study A and 
treatments in Study B. (e.g., trt1 and trt3)

I am not sure on how I should set design and contrasts in Limma to address 
such comparisons (if possible). Maybe someone in the List can give me some 
hints?

Thank you

Ana
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