I've been able to find differentially methylated CpG positions using minfi along with differentially expressed genes using the limma package. What is the next step to determining the relationship between the expression (Agilent 4x44k) and methylation data (Illumina 450k)?
My thought process is as follows:
I have two groups, pre- and post- treatment. I would compare the mean delta beta values for the CpGs associated with each gene with the log fold changes from the expression analysis. If this thought process is correct, how do I make this comparison? If not, what would be the correct approach?
Appreciate any insight!