[BioC] help with limma commands

michael watson (IAH-C) michael.watson at bbsrc.ac.uk
Fri Nov 19 16:38:31 CET 2004

In your example,

topTable(fit2, coef=1, adjust="fdr")

Will get you the diff expressed genes for "group2-group1".

topTable(fit2, coef=2, adjust="fdr")

Will get you the genes for "group3-group2" etc

The key argument here is "coef", which you should use to refer to the
index of the coefficient as specified in the call to makeContrasts.


-----Original Message-----
From: Jeremy Preston [mailto:jpreston at mscience.com.au] 
Sent: 19 November 2004 06:03
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] help with limma commands

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 success.


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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