On Mon, Aug 20, 2012 at 10:42 AM, Brent Pedersen <bpederse@gmail.com> wrote:

>
> > TCGA methylation data is background corrected and dye bias equalized (for
> > the 450k samples, at least, and as batches are updated, 27k as well) but
> no
> > batch correction is done for the level 3 data.  In the case of
> multi-batch
> > tumors it is a good idea to run ComBat or (if you must) SVA to
> compensate.
>
> Sorry to hijack the thread, but, what is the reason to prefer ComBat over
> SVA?


Because in practice, with calibration samples, it seems to work better.


 > 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'm guessing this to be true only for tumor/normal comparisons or
> "pure" samples.
>

Yes, the former typically have distinct cancer-related (vs. tissue-related)
changes if any, and the latter are a bit like unicorn poop (never seen in
the wild).

http://www.nature.com/nbt/journal/v30/n5/full/nbt.2203.html?WT.ec_id=NBT-201205#/methods



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

Funny you should mention this particular task :-)

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0041361

Given the difficulty of isolating gold standard reference populations by
flow sorting, it's tough to benchmark the various transformations, but what
you gain in linearity you may lose in leverage.  Since there isn't one
particular transformation that simultaneously linearizes and stabilizes a
proportion,

http://www.jstor.org/discover/10.2307/1269291?uid=2129&uid=2&uid=70&uid=4&sid=21101141681241

you have to pick your battles.  In the case of compositional analysis, 30+
years after Aitchison and Shen's seminal papers, it appears to remain
unresolved.   The ability to isolate a small number of highly purified
cells and perform targeted BS-seq on picogram quantities of DNA may put
this to rest.

http://leg.est.ufpr.br/lib/exe/fetch.php/pessoais:abtmartins:thestatisticalanalysisofcompositionaldata.pdf

However... joint analysis via DNA methylation and expression (array or
RNAseq) is another matter, and there I have a candidate (in need of
validation).


I can't say that I'm entirely unhappy about you 'hijacking' this thread...

--t

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