[BioC] Limma contrasts question

Daniel Brewer daniel.brewer at icr.ac.uk
Fri Oct 17 11:52:24 CEST 2008


I have three types of samples PC3M (the control cell line), Knockdown
(PC3M with an siRNA knockdown vector) and Scramble (PC3M with a vector
with a scrambled sequence).  I have set up my design matrix like this:

design <- modelMatrix(targets,ref="PC3M")

As one of the comparisons I would like to compare the knockdown vs the
controls.  How would one do this?

Is something like this correct?

contrast.matrix <- makeContrasts("Knockdown vs Controls"=(2*Knockdown -



Daniel Brewer, Ph.D.

Institute of Cancer Research
Molecular Carcinogenesis
Email: daniel.brewer at icr.ac.uk

The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.

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