Question: Batch effect of RRBS data (Methylation): Elimination and Pipleline
3
gravatar for Shicheng Guo
4.9 years ago by
Shicheng Guo8.5k
Shicheng Guo8.5k wrote:

Hi All,

Which kind of pipeline are recommended to be use to eliminate the batch effect of RRBS dataset (DNA methylation)? Combat or Sva? Is there any study to compare different method?

Thanks.

rrbs batch-effect • 1.7k views
ADD COMMENTlink modified 4.4 years ago by david.ashbrook0 • written 4.9 years ago by Shicheng Guo8.5k

Hi, what is the batch effect you're concerned about and how are you planning to model your data? Knowing that I may be able to offer some advice about how to control for the batch effects

ADD REPLYlink modified 4.4 years ago • written 4.4 years ago by Jautis300
0
gravatar for david.ashbrook
4.4 years ago by
david.ashbrook0 wrote:

Hi, Did you get any further with this? I have the same problem, and was wondering if you had the code you eventually used?

Thanks,

ADD COMMENTlink written 4.4 years ago by david.ashbrook0

Hi, Did you get any further with this? I have the same problem, and was wondering if you had the code you eventually used?

ADD REPLYlink written 3.9 years ago by yinzl200720
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