Hello Community, I'm currently encountering an issue while analyzing DNA methylation data using the ChAMP package in R. I'm working with IDAT files from the Infinium MethylationEPIC BeadChip and attempting to load and preprocess the data using champ.load(). However, I've encountered a consistent error that has left me puzzled, and I'm seeking any advice or insights you might offer.

When executing the champ.load()

I encounter the following error: Error in champ.import(directory, arraytype = arraytype) : Meth Matrix and UnMeth Matrix seems not paried correctly.

ChAMP Version: 2.32.0 Microarray Platform Used: EPIC-8v2-0_A1 Annotation File Used: I've relied on the IlluminaHumanMethylationEPICanno.ilm10b4.hg19 for annotation. I'm wondering if this could be a contributing factor to the problem.

I've seen similar issues mentioned here but haven't found a clear solution yet.

You are using an EPIC v2 array but annotating using the EPIC v1 file. I don't use ChAMP myself, so I don't know how you would get around the issue. But if you were to use minfi, you could do this:

library(BiocManager)
## Get the correct annotation files from Zuguang Gu's GitHub
install("jokergoo/IlluminaHumanMethylationEPICv2manifest")
install("jokergoo/IlluminaHumanMethylationEPICv2anno.20a1.hg38")
library(minfi)
rgset <- read.metharray.exp(<args go here>)
annotation(rgset) <- setNames(c("IlluminaHumanMethylationEPICv2","20a1.hg38"), c("array","annotation"))

And then you can carry on as normal.