Batch effect of RRBS data (Methylation): Elimination and Pipleline

Question

[Shicheng Guo]

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.

[Jautis]

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

Answer 1

[david.ashbrook]

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,

[yinzl2007]

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