I am analyzing data (from the TCGA project) of patients affected by Glioblastoma Multiforme and, specifically, I want to compare Gene Expression values with Methylation levels.
Methylation levels have been obtained using Illumina Infinium HumanMethylation27 BeadChip, of which I downloaded the product support file*, that retrieves methylation levels of ~27k CpG sites.
Here comes the issue: for a lot of genes there are several probes (hence, CpG sites) that regulates the same gene. I was wondering what could be the best way to treat them as a unique entity, so to obtain a single methylation level for each gene.
I was thinking of taking the average of all the probes that control one specific gene but the assumption here is "all CpGs have the same importance as gene expression regulators" and I don't know if I can justify it.