[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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