[BioC] Limma contrasts question

James W. MacDonald jmacdon at med.umich.edu
Fri Oct 17 14:32:04 CEST 2008

Hi Dan,

Daniel Brewer wrote:
> Hello,
> 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 -
> Scramble)/2)

I doubt it, but given the amount of information we have here, I can't be 
sure. Please read the posting guide and follow its recommendations. At 
the very least we will need to know what type of arrays you are running 
(I assume spotted arrays of some stripe), and what your targets file 
looks like.



> Thanks
> Dan

James W. MacDonald, M.S.
Hildebrandt Lab
1150 W. Medical Center Drive
Ann Arbor MI 48109-0646

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