[BioC] Variance stabilization of m-values

[Brent Pedersen]

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