I dye-swap with biological , not technical, replicates.

I think dye balance (as in a loop design) is necessary.  Dye swapping 
is not required.
I think that in a reference design, if you are quite sure that the 
reference sample will light up on every spot, then dye swap is not necessary.

--Naomi

At 04:44 AM 2/24/2006, Georg Otto wrote:

>Gordon Smyth <smyth@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
>
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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111

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