I have identified some missing probes on the EPIC array for my analysis using Minfi.
Apparently there is no easy way to update this (no mention about this in tutorial or from google). Naively, I've tried to update the Mset object direct as such:
head(featureNames(Mset))  "cg18478105" "cg09835024" "cg14361672" "cg01763666" "cg12950382"  "cg02115394"
featureNames(Mset) <- all_probes Error in `sampleNames<-`(`*tmp*`, value = c("cg18478105", "cg09835024", : number of new names (866616) should equal number of rows in AnnotatedDataFrame (866150)
Would appreciate if someone could enlighten me. Thanks!