Hi,

I would like to know if there is a package for batch effect correction for RRBS data (or WGBS) like minifi for methylation arrays.

The problem is: I have sequencing data from 2 groups (each group has Control and Treatment subgroups) sequenced and prepared at the same lab, but on different days. And I see that I can not analyse them jointly - PCA/hclust shows me that different groups tend to cluster separately.

Now I am doing the same analysis within 2 groups separately (and report replicated results), but I wish to be able to analyse them jointly to reach higher statistical power.