Hi, I agree with the above mentioned, minfi is a good methylation specific package that includes normalization and quality control while limma allows testing for differential methylation. They work well together and are easy to adapt to your necessities. I use missMethyl: Analysing Illumina HumanMethylation BeadChip Data for the enrichment. They incorporate a batch correction method that works pretty good (consider other methods, e.g. combat too). Integrates nice with minfi and limma and good for visualization too. I hope this enhances the previous response!