Hi Bioc-devel, I recently analyzed a methylation array dataset which is from EPIC array v2.0 ( https://www.illumina.com/products/by-type/microarray-kits/infinium-methylation-epic.html) and currently there is no manifest nor annotation packages for that one. The available packages on Bioconductor are only for EPIC array v1.0:
- IlluminaHumanMethylationEPICmanifest - IlluminaHumanMethylationEPICanno.ilm10b4.hg19 And it is not proper to use the v1 packages for the v2 data. I've built a manifest package and an annotation package for the EPIC array v2.0. They are available at: https://github.com/jokergoo/IlluminaHumanMethylationEPICv2manifest https://github.com/jokergoo/IlluminaHumanMethylationEPICv2anno.20a1.hg38 Basically they are built with the scripts in the original v1 packages, with small adjustment. The scripts for building the two packages are also included in the two packages. The two v2 packages can be seamlessly integrated into the minfi analysis. I also did some simple comparisons between v1 and v2 ( https://jokergoo.github.io/IlluminaHumanMethylationEPICv2manifest/articles/IlluminaHumanMethylationEPICv2manifest.html ). Since the v1 packages were developed by the bioc core members, I want to ask is there any plan to support the EPIC v2 array officially? If there is no such plan, can I submit the two packages to bioc? If I can, then I will have some additional questions regarding how to pass BiocCheck (e.g. file size, lazy loading, ...). But that will be in another email. Best, Zuguang [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel