[BioC] Limma: correct calculation of B statistics (log odds)

[J.delasHeras at ed.ac.uk]

I have been using B values to rank genes in order of more likely to 
less likely (differentially expressed) in LimmaGUI.

I am now using Limma, I noticed the default value for the parameter 
"proportion" (on the function eBayes) is set at 0.01 (expected 1% 
differentially expressed genes). I didn't pay much attention to this 
parameter before, because in LimmaGUI you cannot specify it.

However, now that I use "straight" Limma more I was playing with the 
proportion parameter and it affects the B stats a lot. Therefore I come 
to the question of what's the best way to estimate this parameter.

My first guess is to use the P values (FDR, calculated by BH) to decide 
a cut off, usually 0.05. Then see how many genes are differentially 
expressed according to that rule. And use this observed proportion of 
differentially expressed genes as my proportion parameter.

Is this the correct way to do it?

Jose

-- 
Dr. Jose I. de las Heras                      Email: J.delasHeras at ed.ac.uk
The Wellcome Trust Centre for Cell Biology    Phone: +44 (0)131 6513374
Institute for Cell & Molecular Biology        Fax:   +44 (0)131 6507360
Swann Building, Mayfield Road
University of Edinburgh
Edinburgh EH9 3JR
UK