What if I have a dataset with both EPIC v1 and v2? - genetics-of-dna-methylation-consortium/godmc_phase2 GitHub Wiki

If you have a DNA methylation dataset that has been profiled with both EPIC v1 and v2 arrays then you can QC and normalise it with meffil as one dataset.

qc.objects <- meffil.qc(samplesheet, featureset="epic:epic2", verbose=T)

All the remaining steps are the same. However, you should include chip as a covariate in the analysis.