TCGA Methylation Data CpG Islands

Question

[engineer.khan]

I have been using Methylation data from TCGA, but not getting any clue of matching a record to respective CpG Islands/gene. Can anyone guide there please?

[russhh]

which version of the methylation data have you downloaded? The level-3 data (well, certainly the lung version) contains mappings of the probe ids to gene symbols and to chromosomal positions

[engineer.khan]

Yes level 3 of Breast/Ovary Cancer. Downloaded from ICGC

Answer 1

[Charles Warden]

Last time I checked, TCGA uses 450k data for DNA methylation. You can use the annotation file (.bpm) file to map the probes to CpG islands.

You can get the latest version from Illumina. If you have a hard time tracking it down, I have an annotation file with the demo dataset in the COHCAP package.

[engineer.khan]

Thank you so much. I am going to check it and get back to you