[BioC] Limma: Three biological repeats, one technical repeat

[aculeata at gmail.com]

Hi all

I'm working on data from an Agilent array that has the following design:

Cy3 ~ Cy5
Treated(SampleA) ~ Control(SampleA)
Control(SampleA) ~ Treated(SampleA)
Treated(SampleB) ~ Control(SampleC)
Control(SampleD) ~ Treated(SampleE)

i.e. the first dye swap pair is with the same sample, the second is
with four different samples. What is the correct way to specify the
design?

Thanks in advance!