[BioC] Variance stabilization of m-values

Gordon K Smyth smyth at wehi.EDU.AU
Sat Aug 25 02:35:09 CEST 2012

Dear Brent,

No Amean <- rowMeans(M) wouldn't have the desired effect.  Amean should 
reflect average intensity, so it would be necessary to compute Amean from 
the original intensities used to compute the M-values or beta values.

Note that I don't have any first hand experience with methylation arrays, 
so this is just to suggest something that could be tried.

Best wishes

Professor Gordon K Smyth,
Bioinformatics Division,
Walter and Eliza Hall Institute of Medical Research,
1G Royal Parade, Parkville, Vic 3052, Australia.

On Fri, 24 Aug 2012, Brent Pedersen wrote:

> On Thu, Aug 2, 2012 at 5:19 PM, Gordon K Smyth <smyth at wehi.edu.au> wrote:
>> Use eBayes with trend=TRUE later in the pipeline, then variance
>> stabilization may not be needed.
>> Gordon
> Is that recommendation only for beta values?
> when using M-values as a matrix, fit$Amean is not set so this gives an
> error when using eBayes with trend=TRUE.
> Or should one just manually set fit$Amean = rowMeans(M) ?
> thanks,
> -Brent

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