[BioC] Limma for DNA methylation arrays?
Gordon K Smyth
smyth at wehi.EDU.AU
Sat Nov 30 00:41:15 CET 2013
Hi Tim,
I have never analysed data from any of the newer DNA methylation array
technologies, so you should ask someone who has how well the limma
pipeline seems to work on that type of data.
For example, Alicia Oshlack's group develops methods for methylation
arrays and finds limma useful:
http://genomebiology.com/content/13/6/R44
It seems very reasonable to me to suppose that methylation data has
special variance structures that could be advantageously taken into
account. I doubt though that this means abandoning the empirical Bayes
approach entirely, as it is not very dependent on normality or
independence and gives some benefit in a wide range of situations. You
will notice that I recommended to the original poster that they used
eBayes() with trend=TRUE.
Best wishes
Gordon
On Fri, 29 Nov 2013, Tim Triche, Jr. wrote:
> Is eBayes generally regarded as appropriate for DNA methylation microarray
> probes, i.e. is the general consensus that departure from normality and
> shared variance structure is "normal enough" to shrink towards a global
> prior distribution whose parameters have been estimated from a potentially
> mixed population? e.g. concerns could involve the probe type (paired vs.
> unpaired), variance structure (which with m-values, one assumes these are
> at least approximately normal), and the degree of sharing (e.g. nearer
> probes tend to be more correlated than further probes, and probes in
> certain regions tend to be inherently more variable across datasets than
> probes in other regions).
>
> I've been meaning to ask for your thoughts on this for quite some time :-)
>
> Best,
>
> --t
>
> *He that would live in peace and at ease, *
> *Must not speak all he knows, nor judge all he sees.*
>
> Benjamin Franklin, Poor Richard's
> Almanack<http://archive.org/details/poorrichardsalma00franrich>
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