[BioC] Variance stabilization of m-values

[Wolfgang Huber]

Dear Gustavo

the two issues:
- whether filtering of probes by overall variance is admissible and 
helpful for your analysis
- whether the variance depends on the mean
are unrelated. If I understand your question correctly (and I am not 
sure I do), then you should filter on the overall variance of the M 
values, and need not worry about the mean-variance relationship.

Can you check the paper on this topic ("Independent filtering increases 
detection power for high-throughput experiments", 
http://www.pnas.org/content/107/21/9546.long) and get back if it is 
still unclear?

	Best wishes
	Wolfgang


Aug/3/12 1:19 AM, Gordon K Smyth scripsit::
> 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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