Question: DMRcate: Scaling factor for bandwidth
0
gravatar for alexandria.andrayas
2.7 years ago by
alexandria.andrayas0 wrote:

Hello,

So I am using the DMRcate package to find deferentially methylated regions. Using the dmrcate() function requires a value for C, scaling factor for bandwidth. It states that for 450k data when lambda = 1000 near-optimal prediction of sequencing-derived DMRs is obtained when 'C' is approximately 2. I was wondering if this would be the same for the EPIC array data??

 

Thanks

 

Alex

dmr analysis dmrcate dmr • 641 views
ADD COMMENTlink modified 2.7 years ago by Tim Peters80 • written 2.7 years ago by alexandria.andrayas0
Answer: DMRcate: Scaling factor for bandwidth
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gravatar for Tim Peters
2.7 years ago by
Tim Peters80
Australia
Tim Peters80 wrote:

Hi Alex,

I haven't done any empirical testing on the distribution of EPIC CpGs but I'd wager the optimum is about the same. The real issue is when you're doing sequencing assays, and fitting genomically consecutive CpGs, that you have to make C a lot larger, which makes the kernel smaller. 

If you're concerned, I'd err on the side of making Ca bit bigger, say 3 or 4, since there are more probes on EPIC than 450K. If C is too small, and the kernel is to big, it can rope in nearby CpGs that aren't all that DM, and the DMR endpoints won't be as "precise". The tradeoff, of course, is that inflating C may atomise the DMRs too much, if you're looking for bigger DMRs in the order of kilobase or tens of kilobase, and you prefer these collapsed. But then you can just make lambda bigger if this is a bother! 

Good luck,
Tim

ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by Tim Peters80
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