We have now tested multiple functionalities of the minfi package for the analysis of EPIC arrays. We have performed a comparison of the different normalization methods in minfi, and the results are presented in our recent preprint: http://biorxiv.org/content/early/2016/07/23/065490
Hope this helps,
You would apply some sort of normalization.
Some some normalization strategies may work better for 450k vs EPIC arrays (for example, the proportion of Type I vs Type II probes is different), but I've found that the Illumina normalization seems to work pretty well in both cases.
You can apply Illumina normalization within Genome Studio, or the minfi Bioconductor package using preprocessIllumina(). This applies a background adjustment and normalization to controls.
It would also be best to have multiple samples to compare differential methylation (at the site or region level). For example, if you apply a delta beta threshold of 0.2, that might be greater than the difference in beta values obtained from different normalization methods (although it could affect marginally significant candidates).
The minfi package provides tools for analyzing Illumina's Methylation arrays, specifically the 450k and EPIC (also known as the 850k) arrays.Arrays offer a reliable cost effective way of analysing multiple targets on a large scale. The Genome Centre has offered Illumina methylation arrays since their original golden gate assay. Every student will get any type of academic paper and writing tips from the different resources and make his/her educational life run more smoothly and effectively.