[BioC] Finding and controlling for dye bias in Limma

[Gordon K Smyth]

> 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?

Yes

>  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?

No, the Dye-bias column should be all 1's.

Gordon

> Thanks,
> Sean