[BioC] dye effect in limma

[Dejian Zhao]

Hi,

I have a question about evaluating dye effects in limma.

In chapter 8.1.2 of limma users guide, an example is given to 
demonstrate how to estimate dye effects. The design matrix is 
constructed by the following command:
 >design <- cbind(DyeEffect=1,MUvsWT=c(1,-1,1,-1))
 > design
     DyeEffect MUvsWT
[1,]         1      1
[2,]         1     -1
[3,]         1      1
[4,]         1     -1

In my case, I ignored the dye effects previously. Now I want to correct 
the dye effect. I am wondering  how to build the design matrix.
According to the above-mentioned example, I think adding one column 
(DyeEffect=1) to my previous design matrix will do. Is that right?
 > design <- cbind(DyeEffect=1,design)

Thanks!

Dejian