Hi I am processing methylation data and am having trouble incorporating the new EPICv2 annotation. For now all I want is to read in the data, annotate with the v2 annotation, normalize and write the beta values to a table. Can someone assist with how this can be done?

Many thanks!

I am using R/4.2.2

I don't use ChAMP, so don't know exactly how you would do it, but if you use minfi, here is a post that might be helpful. How to get DMR for Infinium methylation EPIC v2

Hi,

Have you resolved the issue you were facing?

I found this document. It provides information on how to process EPIC V2 data using ChAMP. Based on this description, it seems that you just need to download the latest version of the package and change the "arraytype" parameter from "EPIC" to "EPICv2."

But, even though, I still encountered an error "Error in champ.import(directory, arraytype = arraytype) : Meth Matrix and UnMeth Matrix seems not paried correctly." Have no idea...