I have a quick question and I'm hoping someone can help. I noticed that in the gdac firehose DNA methylation data, there are significantly fewer probes selected from the 450K Illumina methylation arrays than on the TCGA data portal (for example, for HNSC, there are roughly 20K DNA methylation probes in firehose instead of 450k probes, like in TCGA). I am trying to find the documentation on the gdac firehose methylation data in order to see what criteria they used to select these 20K probes out of the 450K, but I am not really finding anything about this yet. Have you come across any documentation that describes this, and if so, could you please send me the link for this?
Thank you in advance!