[BioC] Nonorthogonal multiple comparisons in Limma/ Books on Bayesian Statistics

[Gordon Smyth]

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 Unpublished method though.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