I have two questions.
- Does anyone knows which tool is the best for Methylation EPIC array analysis? Something as useful as ChAMP.
I know minfi package can help in loading and normalising data. But I also have to filter probes based on SNPs overlap, detection p.value, and so on (similar as all the steps given in champ.load function).
So how should I go about doing it?
I thought to load data with minfi package (not through champ.load) -> filter using champ.filter -> normalize using champ.norm (method =SWAN).
Does it make sense?
2 Also which normalisation method is preferred SWAN or BMIQ? In literature search, I found both as closely equivalent but if I am missing something for data type please correct me.
If any one has prior experience or suggestions please let me know.