Beginner differential methylation analysis

Question

[a.basitkhan1990]

Hi all!

I have a set of IDAT files from patient tumors with two conditions (condition a and b).

Could you please advise how to do a basic differential methylation analysis in R. Specifically, what is the optimal pipeline or package to use?

Thanks!

[Basti]

There is a lot of methylation tutorial available on the Internet :

• minfi : https://www.bioconductor.org/help/course-materials/2015/BioC2015/methylation450k.html
• methylKit : https://bioconductor.riken.jp/packages/3.5/bioc/vignettes/methylKit/inst/doc/methylKit.html
• ChAMP : https://www.bioconductor.org/packages/devel/bioc/vignettes/ChAMP/inst/doc/ChAMP.html#section-introduction