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

Naomi Altman naomi at stat.psu.edu
Tue Sep 22 15:10:43 CEST 2009

You still need to indicate the biorep and use it as a block, even if 
only one biorep has a replicate.

At 09:55 PM 9/21/2009, Marcelo Laia wrote:
>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
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
>Search the archives: 

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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