how to treat the value of methylation array

Question

[huitianli009]

hello, i download a methylation array result from TCGA, the data level is 3, I found my aim gene having 25 values for corresponding probes in one tissue sample. How to combine these values to one value? I tried mean and median analysis, any of which is not the value got from cBioportal for this gene methylation value in the same sample. as i want to know the relationship between a aim gene expression with methylation status.how to process data and how cBioportal manage these? Thanks a lot!

[Devon Ryan]

Do you really think that assigning a single methylation value to a gene makes much biological sense? If cBioportal does such a thing, do you really think you should trust that for anything?

[huitianli009]

@Devon Ryan, Sorry, i don't know what you mean. could you explain more? thank you very much!

[Devon Ryan]

The average methylation of a gene isn't terribly informative. What matters isn't just the methylation level, but also where it occurs. For example, increased methylation around the TSS will generally decrease gene expression. Increased methylation over the gene body will generally increase expression.