[BioC] Differentially Expressed Genes using Limma

James W. MacDonald jmacdon at med.umich.edu
Wed Sep 2 17:51:42 CEST 2009

Hi Marcos,

Marcos Pinho wrote:
>   Dear List,
> I have been trying to use limma to identify differentially expressed genes
> but have been finding some difilcuties in creating a basic model.matrix. and
> establishing a contrast. I usually have two different types of RNA in
> triplicates, a reference an an experimental and wish to see genes
> differentially expressed between the them. Following the limma manual my
> model.matrix would be:
> design <- model.matrix (~ -1 + factor (c (0,0,0,1,1,1)))
> Could it be done this way???

Yes, but you could use a simpler parameterization.

> In such case, what would be the best way to fit a contrast between my
> reference and experimental???

If you use the treatment contrasts parameterization, the second 
coefficient will be the difference between the two sample types, so you 
don't need a contrasts matrix.

design <- model.matrix(~ factor(rep(1:2, each = 3)))
fit <- lmFit(<data>, design)
fit2 <- eBayes(fit)
topTable(fit2, coef = 2)

> Any help would be greatly appreciated!
> best regards,
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James W. MacDonald, M.S.
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618

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