I am using Illumina methylation arrays for my project. I needed some help regarding the same. Kindly help me on how to go about this. If you could find time and guide me stepwise that would be very helpful.
this would be a good starting point: https://f1000research.com/articles/5-1281/v2
As stated in this paper, there are a few R packages for this type of analysis.
The minfi package has functionalities for the raw data (IDAT files), background correct, normalize, filter probes, adjust for cell counts (if need be), perform CpG and region level differential methylation analysis (through Limma and bumphunter).
A “competing” solution to minfi is ChAMP, which implements different container classes and precessing methods, although it relies on some of minfi’s infrastructure.