[BioC] How to pool subgroups for makeContrasts() and subsequent limma analysis?

René rene.boettcher86 at googlemail.com
Wed Jan 23 10:14:31 CET 2013


Dear all,

My current analysis revolves around various groups and their subgroups, 
which is why I would like to know how I can pool two or more subgroups 
in a contrast matrix.
As an example, let us assume I have 4 main groups (A, B, C and D), of 
which one can be subdivided into 3 subgroups (B1, B2 and B3), hence

groups = c("A","B1","B2","B3","C","D")

Now, I would like to compare the combined/pooled group B (consisting of 
B1, B2 and B3) against all other groups,

B vs A, B vs C, B vs D.

So my question is: how do I formalize that with makeContrasts() for an 
analysis with limma?
If it would be different matrices, I would just use cbind(), however I 
am not sure whether B1+B2+B3 does the same thing in makeContrasts().

Thank you in advance and best regards



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