[BioC] Limma contrasts question

James W. MacDonald jmacdon at med.umich.edu
Mon Oct 20 17:40:19 CEST 2008

Daniel Brewer wrote:
> Thanks for that information.  Yes I did mean PC3M as a contol ... doh.
> Unfortunately I am still having problems.
>> contrast.matrix <- makeContrasts("KvC" = Knockdown - (Scramble +
> PC3M)/2, levels = design)
> Error in eval(expr, envir, enclos) : object "PC3M" not found
> I believe this is because PC3M is not in the design matrix as I am using
> it as the reference.  As a structure for this I have been using the
> direct 2-color design example of the "Limma User guide" (Section 7.4).
> There is a discrepancy between the straight comparisons that you have
> given me and the example in the guide.
> Your suggestion:
> contrast.matrix <- makeContrasts("KvsC" = Knockdown - PC3M, levels = design)
> Their suggestion:
> contrast.matrix <- makeContrasts("KvsC" = Knockdown, levels = design)
> I think this will have something to do with PC3M being described as the
> reference (the intercept in the linear model???) in their approach but
> maybe you use a different reference.  Not sure.

Oh yeah. Sorry - I didn't look closely at the design matrix. I don't do 
two color stuff so this doesn't come second nature to me.

Anyway, I think your original contrasts matrix should be OK. 
Algebraically (2*Knockdown - Scramble)/2 should equal Knockdown - 
(Scramble + PC3M)/2. Sorry for the noise.



> Many thanks for your time.  I really would like to get an understanding
> of this.
> Thanks
> Dan

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

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