Dear List,

I would like to ask a question about using limma package to compare
multiple groups.
As I understand, if I use multiple testing method "separate", I will not
have a p-value correction for testing multiple contrasts, since this method
does multiple testing for each contrast separately. If I use "method =
global", all tests are combined into a long vector of tests, and therefore
all tests are treated as equivalent regardles whether they relate to probe
or contrast. For the other two methods (hierarchical and nestedF), their
properties are not well understood with adjustment "BH".
Therefore, I was planning to use F.p.value (moderated F-statistic), and to
correct it for multiple testing with BH. However, this will only provide me
with one p-value related to all pair-wise comparisons (all contrasts) for
one probe set, and won't point out in which pair-wise comparisons exactly
this probe set is differentially expressed. If I were to use ANOVA
analysis, I would've used a post-hoc procedure in order to find an answer
to this question, however I am not sure how to proceed with the methods
offered by limma package.

Can anybody, please, explain to me how can I perform a procedure similar in
its meaning to post-hoc test in order to find exactly between which groups
are the probe sets differentially expressed?

Thank you very much!

Anna Dvorkin-Gheva

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