[BioC] Finding and controlling for dye bias in Limma

[Sean Davis]

We have several samples hybed on two-color arrays (treated versus 
untreated).  Half are in dye-swap.  Can we use Limma to estimate the 
effect of dye-bias?  A design matrix might look something like:

Array	Treatment	Dye-bias
1		1		0
2		1		0
3		1		0
4		1		0
5		-1		1
6		-1		1
7		-1		1
8		-1		1

The second coefficient would be significant for "dye-biased genes" 
while the first would be treatment effect while controlling for dye 
bias?  Do I understand correctly?

Thanks,
Sean