[BioC] limma user's guide example

[James W. MacDonald]

Hi Giovanni,

Giovanni Coppola wrote:
> Sorry guys, another DQ (dumb question)....
> Limma User's Guide pag. 39 and 42, line:
> cont.matrix <- makeContrasts(MUvsWT=WT-MU, levels=design)
> Why not MU-WT?

It doesn't matter, really. I generally do what you suggest because then 
a positive log difference indicates up-regulation in mutant and negative 
indicates down-regulation. This seems to be more intuitive for my 
Biologist friends. However, other than the sign of the statistic, there 
is no difference.

Best,

Jim


> Thanks
> Giovanni
> 
> 
> 
> 	[[alternative HTML version deleted]]
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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