[BioC] RRBS question

Alex Gutteridge alexg at ruggedtextile.com
Wed Jan 22 11:15:46 CET 2014

On 21.01.2014 20:48, Gilgi Friedlander wrote:
> Hi Alex,
> Sorry to bother you, but I have a question regarding RRBS analysis.
> I saw your post from last year, and also was wondering if bsmooth can
> work well for RRBS data, as going to work on such data.
> I wanted to reply to the post on the mailing list, but didn't see
> such an option.
> If you already have results, and can share your experience if one can
> use bsmooth for RRBS, it will be great. And if not, if you have
> recommendations for other tools.
> Thanks a lot,
> Gilgi

cc'ing the list for future reference and in case anyone else has 
additional insights on RRBS analysis with Bioconductor:

Hi Gilgi,

I had mixed results with bsmooth and rrbs data when I tried it. 
Certainly the various smoothing parameters required tweaking before it 
would run successfully. I can let you know what worked for me, but I'd 
be lying if I said I arrived at them through careful experimentation. 
One also has to be cautious I think about the overall approach of 
whether smoothing makes sense when the data from rrbs is by definition 
non-contiguous. That said, bsmooth did run and did detect differential 
methylated regions for us which looked correct on deeper inspection. 
What bsmooth (by design I guess) does not detect are the single CpGs 
that seem to change between experimental groups, but sit within larger 
regions that clearly do not change. It's still an open question (in my 
mind at least) whether such sites are likely to be biologically 
significant or not.

Alex Gutteridge

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