[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.

contrast <-makeContrasts(

        (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


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