[BioC] Limma, dye-swaps and uneven numbers of replicate arrays

[michael watson (IAH-C)]

Hi

A simple question really - I have five biological replicate RNA samples.
Each will have cells untreated vs treated, so that's five arrays.  I
want to do dye-swaps, but that means I can have 2* Cy5/Cy3, and 3*
Cy3/Cy5. Do I need to compensate for this "imbalance"?  How do I do it
in limma?

Thanks
Mick