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

aculeata at gmail.com aculeata at gmail.com
Thu Jan 14 20:03:02 CET 2010

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

Thanks in advance!

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