On Mon, Jan 31, 2011 at 9:57 AM, Richard Friedman <
friedman@cancercenter.columbia.edu> wrote:

> 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.
>
>
Hi, Richard.

Have a look at this publication which recommends forming ratios:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3012676

Sean

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