[BioC] base of B-value log in Limma - still not sure

[Richard Friedman]

Gordon,

	Thank you very much. i am sorry that I missed it in the user's guide.

Best wishes,
Rich
On May 6, 2006, at 6:31 AM, Gordon Smyth wrote:
> The answer to this question is in Section 10.1 ("Output from eBayes") 
> of the Limma User's Guide, where it is explained explicitly how to 
> convert from the B-statistics into probabilities.
>
> In R and in mathematics, log() always means base-e unless otherwise 
> stated. Other disciplines may be less precise, but all math stat 
> journals that I know of follow this convention.
>
> The use of base-2 for M-values is a reference to 2-fold-changes, which 
> have a traditional meaning. There is no such interpretation for 
> probabilities or odds-ratios, hence no reason to use base-2 for the 
> B-statistics. In any case, the B-statistic was defined by Lonnstedt 
> and Speed (2002), and it is not appropriate for limma to change the 
> definition.
>
> Best wishes
> Gordon
>
------------------------------------------------------------
Richard A. Friedman, PhD
Associate Research Scientist
Herbert Irving Comprehensive Cancer Center
Oncoinformatics Core
Lecturer
Department of Biomedical Informatics
Box 95, Room 130BB or P&S 1-420C
Columbia University Medical Center
630 W. 168th St.
New York, NY 10032
(212)305-6901 (5-6901) (voice)
friedman at cancercenter.columbia.edu
http://cancercenter.columbia.edu/~friedman/


"Cartesian duelism is when somebody told Decartes that he didn't think
therefore he was, and Descartes challenged him to a duel".
-Isaac Friedman, age 16