[BioC] Multi-level experiments

[Yu Cai [guest]]

Dear Limma Experts:
I am currently working on a project that has exactly the same design as the example given in Section 9.7 multi-level experiments of Limma package's user guide. But our questions about the contrasts are slightly different: 1) what's the overall difference between disease and normal regardless of tissue types, and 2) what's the overall difference between tissue A and tissue B regardless of whether diseased or normal?

Here is my modification to the contrasts in attempt to answer our questions:

cm <- makeContrasts(
	+ DiseasedvsNormal = (Diseased.A-Normal.A + Diseased.B-Normal.B)/2,
	+ TissueBvsTissueA = (Normal.B-Normal.A + Diseased.B-Diseased.A)/2,
	+ levels = design);

Am I right?
Tremendous thanks for your help.

Yu Cai



 -- output of sessionInfo(): 

 

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