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

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
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updated by david.ashbrook • david.ashbrook • written by Shicheng Guo Shicheng Guo

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

• 1 views • link
written by Jautis Jautis

1 answer

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,

• 0 views • link
written by david.ashbrook • 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?

• 0 views • link
written by yinzl2007 • yinzl2007

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