Question: Nonorthogonal multiple comparisons in Limma/ Books on Bayesian Statistics

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15.2 years ago by

Gordon Smyth ♦

**38k**Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia

Gordon Smyth ♦

**38k**wrote:At 03:12 AM 6/08/2004, Richard Friedman wrote:
>Fellow Expressionists,
>
> Does Limma automatically perform a multiple
>comparison adjustment for non-orthogonal contrasts?
Yes. classifyTestsF() is a classification which takes full account of
non-orthogonality. Unpublished method though. Also "holm" and some
other
options are valid even across non-orthogonal contrats.
> If not, can you recommend another program that can
>be used in conjunction with Limma to do this?
>
> Also, I find the Bayesian theory in the paper
>by Gordon Smyth ("Linear Models and Empirical
>Bayes Methods..." tough going) Can anyone
>please recommend a book or books on Bayesian methods
>that can bridge the gap between basic statistics texts
>(e.g. Hoel, "An Introduction to Mathematical Statistics" and
>Zar "Biostatistical Analysis" and this article)?
I don't know of any accessible refs, even for stat majors I'm afraid.
And
unfortunately Bayes refs may not be much help. The empirical Bayes
arithmetic requires different quantities to be computed compared to
full Bayes.
I hope that the final formula in the paper make intuitive sense even
though
the math derivation might be hard.
Gordon
>Thanks and best wishes,
>Rich