Question: Variance stabilization of m-values

0

7.4 years ago by

Gordon Smyth ♦

**39k**Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia

Gordon Smyth ♦

**39k**wrote:Use eBayes with trend=TRUE later in the pipeline, then variance
stabilization may not be needed.
Gordon
> Date: Wed, 1 Aug 2012 15:20:56 +0200
> From: Gustavo Fern?ndez Bay?n <gbayon at="" gmail.com="">
> To: bioconductor at r-project.org
> Subject: [BioC] Variance stabilization of m-values
>
> Hi everybody.
>
> I am working with Illumina 450k methylation data. I am currently
> cleaning a data set, getting rid of XY probes, etc? and I would like
to
> do a non-specific filtering and preserve only 20% of the probes,
those
> with the higher variability (as seen in Chapter 7 of the
Bioconductor
> Case Studies book).
>
> In the book, they create a meanSdPlot() and proceed as the variance
is
> not dependent on the mean (to a significant degree).
>
> Trying to follow that procedure, I have converted my beta values to
> M-values, and then called meanSdPlot(). It shows, for my data, that
> there is a relationship between mean and variance, i.e. the line
with
> the median is not horizontal. Of course, if I create a meanSdPlot
with
> the beta values, the effect is greater, due to their
heteroscedasticity.
>
> Question: Is it correct to use a variance stabilization
transformation
> (as the one in justvsn) on the M-values in order to discard low-
variance
> probes?
>
> Any hint will be much appreciated.
>
> Regards,
> Gus
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modified 7.3 years ago
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Brent Pedersen •

**90**• written 7.4 years ago by Gordon Smyth ♦**39k**