[BioC] transformation for illumina methylation beta data prior to input to limma

[Richard Friedman]

Dear List,

	The following question was asked before before but I do not believe  
that an answer was given:
Should Illumina methylation beta data be transforrmed before input  
into Limma.
Beta values are between 0 and 1.
In ordinary frequentist statistics variables which range between 0 and  
1 are subject to a logistic
transformation before anova is applied to them (more precisey a  
general linear model is used with
a logistic link function and a binomial error model).
Should
A.  A logistic transformation be applied before inputing methylation  
beta data into Limma.
or
B. Should a log transformation be applied.
or
C. Should some other transformation be applied.
or
D, Should no transformation be applied.

I would greatly appreciate any insight that you might have into this  
problem.

Thanks and bet wishes,
Rich

------------------------------------------------------------
Richard A. Friedman, PhD
Associate Research Scientist,
Biomedical Informatics Shared Resource
Herbert Irving Comprehensive Cancer Center (HICCC)
Lecturer,
Department of Biomedical Informatics (DBMI)
Educational Coordinator,
Center for Computational Biology and Bioinformatics (C2B2)/
National Center for Multiscale Analysis of Genomic Networks (MAGNet)
Room 824
Irving Cancer Research Center
Columbia University
1130 St. Nicholas Ave
New York, NY 10032
(212)851-4765 (voice)
friedman at cancercenter.columbia.edu
http://cancercenter.columbia.edu/~friedman/

"Did he win the Nobel prize or the Ig Nobel
prize for levitating the frog?".
Rose Friedman, age 14