Illumina methylation EPIC V2 array

Question

[juliviglino]

Hi, Im analyzing methylation data from the new illumina's EPIC V2 array (930K).

I would like to perform enrichment analysis. In the past, I have always used missMethyl but since there are a lot of differences between EPIC V1 and EPIC V2 arrays I'm unsure if missMethyl can be used (Im afraid results might be biased)

Does anyone know any enrichment tool already available for the EPIC V2 array?

Thanks

Answer 1

[fu_entomology]

We have been using SeSAMe, it works well for the most part. They have an enrichment tool called KnowYourCG. You can check it out their vignette: https://www.bioconductor.org/packages/release/bioc/vignettes/sesame/inst/doc/KYCG.html. Note, SeSAMe and Minfi (and that suite of packages) have different data structures; However, for enrichment analysis, you only need probe IDs. Then you can use either curated databases from SeSAMe, or you can simply extract gene information, and run gprofiler2 as shown at the bottom part of the link I shared. Hope this helps.