[BioC] help with limma commands

Jeremy Preston jpreston at mscience.com.au
Fri Nov 19 07:03:00 CET 2004

Hi there,

I was wondering what command to use to see the lists of genes for
group3-group2 and group3-group1.

In the example from the user guide the top genes expressed differentially in
group2 versus group1 can be obtained with the command listed below. I have
tried to extrapolate this to get the other contrasts, but have had no


To make all pair-wise comparisons between the three groups the appropriate
contrast matrix can be created by

> contrast.matrix <- makeContrasts(group2-group1, group3-group2,
group3-group1, levels=design)
> fit2 <- contrasts.fit(fit, contrast.matrix)
> fit2 <- eBayes(fit2)

A list of top genes differential expressed in group2 versus group1 can be
obtained from

> topTable(fit2, coef=1, adjust="fdr")
Any help on this matter would be greatly appreciated.



Jeremy Preston, PhD

Applications Scientist


Millennium Science  <http://www.mscience.com.au> www.mscience.com.au

2/390 Canterbury Road, Surrey Hills, Victoria 3127 Australia

mob: 0407 742 426 | office: +61 3 9830 7922 | fax: +61 3 9830 7933

jpreston at mscience.com.au   support at mscience.com.au




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