[BioC] help with limma contrast matrix
Kimpel, Mark W
mkimpel at iupui.edu
Tue Nov 9 17:54:55 CET 2004
I would appreciate advice on how to construct a contrast matrix for a
5X2 ANOVA design. Briefly, I have a genomic experiment to analyze that
compares 5 brain regions in 2 strains of rats. We are interested in
discovering overall differences between strains (collapsing all brain
regions together) but also discovering differences that may only be
expressed in one brain region.
I have attempted to construct the appropriate matrix with the code
listed below, but it does not work. I seem to get differences between
strains, but all the brain region contrasts give exactly the same
results, so I know something isn't correct.
(NPAccumbens + NPAmygdala + NPHippocampus + NPPrefrontal_Cortex
+ NPStriatum) - #all regions of strain "NP"
(PAccumbens + PAmygdala + PHippocampus + PPrefrontal_Cortex +
PStriatum) #all regions of strain "P"
(NPAccumbens - PAccumbens),
#accumbens region of both strains
(NPAmygdala - PAmygdala),
#amygdala region of both strains
(NPHippocampus - PHippocampus),
#hippocampus region of both strains
(NPPrefrontal_Cortex - PPrefrontal_Cortex),
#Prefrontal_Cortex region of both strains
(NPStriatum - PStriatum),
#striatum region of both strains
Mark W. Kimpel MD
(317) 490-5129 Home, Work, & Mobile
(317) 278-4104 FAX
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