[BioC] limma technical replicates and biological replicates in the same design

Marcelo Laia marcelolaia at gmail.com
Tue Sep 22 03:55:29 CEST 2009


On the limma usersguide I found the example:

FileName Cy3 Cy5
File1 wt1 mu1
File2 wt1 mu1
File3 wt2 mu2
File4 wt2 mu2

where two wild-type and two mice from the same mutant strain are
compared using two arrays for each pair of mice.

> biolrep <- c(1, 1, 2, 2)
> corfit <- duplicateCorrelation(MA, ndups = 1, block = biolrep)
> fit <- lmFit(MA, block = biolrep, cor = corfit$consensus)
> fit <- eBayes(fit)
> topTable(fit, adjust = "BH")

I have something like this, but, in my case, I have:

FileName Cy3 Cy5
File1 pra1 banha1
File2 pra1 banha1
File3 pra2 banha2
File4 pra3 banha3

banha is my reference and pra is my tester.

Only the two first is technical replicates. The others two are
biological replicates.

How I could dealing a design for my situation?

Thank you very much.

Marcelo Luiz de Laia
Universidade do Estado de Santa Catarina
UDESC - www.cav.udesc.br
Lages - SC - Brazil
Linux user number 487797

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