[BioC] Limma: technical replicates in multi-group design

Wei Shi shi at wehi.EDU.AU
Thu Mar 25 23:37:26 CET 2010

Dear Adam:

    You can use the following commands to create a design matrix for 
your experiment:

s <- factor(c("A","A","B","B","C","C"))
design <- model.matrix(~0+s)
colnames(design) <- levels(s)
fit <- lmFit(x,design)

    To do a pairwise comparison, you can use the makeConstrasts function:

contr <- makeContrasts(A-B,A-C,B-C,levels=design)
fit.contr <- eBayes(contrasts.fit(fit,contr))


Adam Kiezun wrote:
> Hi,
> How do I write the design matrix to specify technical replicates in
> multi-group experiment on a single-channel array (data coming from
> lumi)?
> I have 3 groups of samples (A, B, C), each group has 2 technical
> replicates (so I have 6 expression vectors: A1, A2, B1, B2, B3). How
> do I write the design matrix to tell limma that A1 and A2 etc are
> technical replicates and that I want to do all pairwise comparisons
> between groups (ie. AvsB, AvsC, BvsC)?
> The limma manual covers technical replicates for two-channel arrays,
> and the multi-group experiments with biological replicates. I'd like
> to know how to deal with a one-channel arrays, multi-group experiment
> with technical replicates.
> regards
> Adam
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