getUnMeth() didn't work for EPIC v2

[atomnh]

I applied minfi on EPIC v2, which has been released recently. I realized that most beta values from getBeta() are NA. I checked the output of getMeth(), only 8% of the probes were NA, however, for getUnMeth(), around 90% are NA, I believed that's the reason for that error. But I don't know how to extract the code for getUnmeth() and getMeth(). Could you please help me fix this issue or send me the code that I can modify it by myself possibly? Thank you so much!
Given the EPIC v2 has been released, would you consider to upgrade minfi for that platform? It's really a big pain trying to modify it by myself. Thank you again!

[votti]

For me using the annotations/manifest released here worked to get EPIC v2 running: https://stat.ethz.ch/pipermail/bioc-devel/2023-March/019518.html

1. Install the manifest/annotation

BiocManager::install("jokergoo/IlluminaHumanMethylationEPICv2manifest")
# or
remotes::install_github("jokergoo/IlluminaHumanMethylationEPICv2manifest")

# and
BiocManager::install("jokergoo/IlluminaHumanMethylationEPICv2anno.20a1.hg38")
# or
remotes::install_github("jokergoo/IlluminaHumanMethylationEPICv2anno.20a1.hg38")

2. Change set the annotation metadata of the RGset

RGset = read.metharray.exp(...)

annotation(RGset)["array"] = "IlluminaHumanMethylationEPICv2"

# explained in the IlluminaHumanMethylationEPICv2anno.20a1.hg38 package
annotation(RGset)["annotation"] = "20a1.hg38"

[ABanaeiEsfahani]

Hi Vito @votti,
Hope this message finds you well.
Thanks for the comment. I have already used "IlluminaHumanMethylationEPICv2anno.20a1.hg38". Do you also have any normalisation in your pipeline? Something like "preprocessFunnorm" or "preprocessIllumina". It seems they don't work well here. And as far as I understood, it goes back to the utils.R file (https://github.com/hansenlab/minfi/blob/devel/R/utils.R) where the annotations have been hardcoded. Any comment on this? Have you revised the utils.R file?

i)
.default.epic.annotation <- "ilm10b4.hg19"
ii)
.metharray.types <- c("IlluminaHumanMethylation450k",
"IlluminaHumanMethylationEPIC",
"IlluminaHumanMethylation27k",
"IlluminaHumanMethylationAllergy",
"HorvathMammalMethylChip40")
iii)
.isEPIC <- function(object) {
annotation(object)["array"] == "IlluminaHumanMethylationEPIC"
}