I am not very familiar with RRBS data but if you observe the batch effects
on the pcs you should be able to apply sva directly. If the data are
constrained to be positive you might consider svaseq.
If you already know the batch effect variable you could use Combat or
Hope that helps
On Fri, Mar 10, 2017, 6:26 PM frodrgs2 [bioc] <email@example.com>
> Activity on a post you are following on support.bioconductor.org
> User frodrgs2 <https: support.bioconductor.org="" u="" 9433=""/> wrote Question:
> Using SVA with RRBS data <https: support.bioconductor.org="" p="" 93722=""/>:
> I have seen a lot of posts with this question, but have not found an
> answer to this. I am analyzing my RRBS data with methylKit, and I can see
> in my PCA plots that there are some batch effects.
> Is there a way to use SVA to estimate surrogate variables from methylation
> data? If yes, how to do that properly?
> I have used it before with RNA-seq data, but am not sure on how to use
> with methylation data.
> Thank you!
> Post tags: sva, RRBS
> You may reply via email or visit Using SVA with RRBS data