[BioC] Another question about dye swap

[Ron Ophir]

Hi,
>From limma user guide section 8.1.2 Simple comparisons -> Dye swaps it
is clear that for the following experimental design:
FileName Cy3 Cy5
File1        wt mu
File2        mu wt
File3        wt mu
File4        mu wt
*(four replicates of two groups (wt , mu) of which two replicates in
each group is labeled by one color(red) the other two is labeled by
another color (green)) 
one can estimate the Dye effect by defining that effect as the
intercept :
 design <- cbind(DyeEffect=1,MUvsWT=c(1,-1,1,-1))
 fit <- lmFit(MA, design)
 fit <- eBayes(fit)
 
Let's say that one finds that the Dye effect (for all genes) is
statisticaly insignificant. Would it be correct than to force the model
to go through the intercept by

design <- cbind(DyeEffect=-1,MUvsWT=c(1,-1,1,-1))

Will I get a better estimation of the Mu to wt ratio?

Thanks,
Ron