[BioC] nested design in limma?

[Georg Otto]

Gordon Smyth <smyth at wehi.edu.au> writes:

>
> Just as an aside, I am continually amazed at how common technical 
> dye-swaps are. As far as I can see, they just complicate the analysis 
> to no advantage, yet they have captured the imagination of many 
> biologists. My guess is that this an attempt to balance the dyes, 
> although this can be better achieved without introducing technical replication.


This is an interesting point, since I am going to design and analyse
two-colour experiments soon and I am interested in what people think
about it. Do you recommend dye-swapping with biological replicates? Or
no dye-swapping at all?

Best,

Georg