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

[Wolfgang Huber]

Dear Anonymous,

you could try with reading the "Two color" chapter of the "Bioconductor 
Case Studies" book (Hahne et al., 2008).

	Best wishes
	Wolfgang


aculeata at gmail.com scripsit 01/14/2010 08:03 PM:
> 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!
> 
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--
Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber/contact