Question: limma technical replicates and biological replicates in the same design
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gravatar for Marcelo Laia
9.8 years ago by
Marcelo Laia430
Brazil
Marcelo Laia430 wrote:
Hi, 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
limma santa • 635 views
ADD COMMENTlink modified 4 weeks ago by Gordon Smyth37k • written 9.8 years ago by Marcelo Laia430
Answer: limma technical replicates and biological replicates in the same design
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gravatar for Gordon Smyth
4 weeks ago by
Gordon Smyth37k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth37k wrote:

https://support.bioconductor.org/p/29691/

ADD COMMENTlink written 4 weeks ago by Gordon Smyth37k
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