I'm using the minfi package, taking all the usual steps to analyze my 850k arrays. Without even doing any sort of processing/analysis, I have questions surrounding how probes that overlap different genes or transcripts are handled.

I want to be able to ask questions like, "What is the mean methylation value of all probes within the TSS200 of <gene X>?"

We can use the annotation columns UCSC_RefGene_Name/Accession/Group to help answer, but it's complicated when one probe can be classified as (e.g.) TSS200 or 1stExon, in the same gene due to different transcripts.

Attempt at illustrating this problem below:

what is generally done for these many, many cases?