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.