[BioC] RRBS question

Gilgi Friedlander gilgi.friedlander at weizmann.ac.il
Wed Jan 22 21:01:24 CET 2014

Thank you so much for all the help and important information!

-----Original Message-----
From: Alex Gutteridge [mailto:alexg at ruggedtextile.com] 
Sent: Wednesday, January 22, 2014 7:06 PM
To: Kasper Daniel Hansen
Cc: Gilgi Friedlander; bioconductor at r-project.org
Subject: Re: [BioC] RRBS question

Yes, this is exactly what I found. I ended up tweaking maxGap to 10kbp which seemed to give a reasonable result over most regions.

Alex Gutteridge

On 22.01.2014 16:29, Kasper Daniel Hansen wrote:
> Because RRBS data is non-contiguous, you basically have to use the 
> 'maxGap' argument to do the smoothing on each of the contiguous 
> groups.  You probably also have to use 'local.correct=FALSE' as the 
> algorithm is currently written.  I have not yet experience with 
> applying the algorithm to RRBS data myself.
> Best,
> Kasper
> On Wed, Jan 22, 2014 at 5:15 AM, Alex Gutteridge  wrote:
>> 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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Alex Gutteridge

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