> What about peripheral blood where one may be measuring a signal from a variety
of cell types or tissues?

This would probably prove useful to you - I've played around with it, and
~450 of their training set probes are on the 450k. You can email the
authors for their code.
http://www.biomedcentral.com/1471-2105/13/86/abstract

>switching from 0.1% methylated to 99.9% methylated is probably a real effect.
 Switching from 1% to 3% across the board is probably technical artifacts.
I think its unclear what these effects do (if anything). Effect sizes less
than 1% (which get published) are probably less likely to be real, but
these 1-3% effect size hits often replicate in external populations, even
if the cpg has no effect on gene expression.

-Andrew

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