[BioC] Contrast matrix in limma

[Ingunn Berget]

Dear BioC-list

I have data from a microarray experiment comparing 12 different growth conditions for bacteria. 

This are the conditions 
BC7ppm BC9ppm CH3COOH EtBr EtOH Glycerol gr15 gr46 HCl NaCl NaOH PK

PK is the normal condition and it is of interest to find genes that are differentially expressed in PK and the other conditions. The experiment is a reference design with common reference for all arrays, and with three biological replicates from each condition. The reference is always labelled Cy3. The two conditions BC7ppm and BC9ppm represent the same medium for the bacteria, but with different concentrations of something. 

If I have understood the limma usermanual correctly, the following lines will make all contrasts for comparing gene epression in one condition with PK such that the contrast names BC7.PK compares geneexpression in BC7ppm condition with PK and BC9.PK gene expression in BC9ppm with PPK. 
D <- modelMatrix(MA$target,ref = "Ref") #MA is the MAlist with the normalised data

contrast.matrix <- makeContrasts(gr15.PK=gr15-PK,gr46.PK=gr46-PK,NaCl.PK=NaCl-PK,EtBr.PK=EtBr-PK, EtOH.PK=EtOH-PK,NaOH.PK=NaOH-PK,CH2COOH.PK=CH3COOH-PK,HCl.PK=HCl-PK,BC7.PK=BC7ppm-PK, BC9.PK=BC9ppm-PK, Gly.PK=Glycerol-PK,levels=D)

Since there is very little difference between BC7ppm and BC9ppm, I want to "merge" these to experiments and make one contrast for both. So my questions are

1) can I do this?

2) In general the sum of the coefficients in a contrast should be one, does this mean that I should use something like

BC.PK= 0.5*BC7ppm+0.5*BC9ppm-PK 

as an argument in the makeContrasts command? 



Best regards 

Ingunn



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