[BioC] [Limma] Correcting Dye swap effect

[Ron Ophir]

Hi,
In Chapter 8.1.2 in Limma users guide there is a description how to
detecting the Dye effect. 
The example there describes an experiment of Wt vs Mut with two dye
swaps replicates as follow:

FileName Cy3 Cy5
File1        wt mu
File2        mu wt
File3        wt mu
File4        mu wt

Let's say that I found a list of gene which are significant due to
mutant effect and due to dye effect as well. Can I only ignore them or
can I correct the dye effect?
I guess that it depends how the dye swaps replicates was prepared. If
the dye replicates are technical replicates using the block design is
enough to correct dye effect. If dye replicates are also biological
replicates they night also represent a batch effect. That is all first
replicates was sent in one day and the second replicates sent in another
day, which this difference by itself without dye swap may be a source
for variation. The second option of dye swap preparation may be
corrected by ANCOVA (?). Is possible to do it with LIMMA? I know that a
question about using ANCOVA with LIMMA arose by Naomi Altman but this
discussion was beyond my knowledge. So back to my questions: Is
correcting the dye effect is possible in LIMMA? Is ANCOVA is a solution?
and HOW?

I hope these questions are in the focus of that mailing list,
Thanks
Ron