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TCGA Methylation Data CpG Islands

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?

gene
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updated by Ram Ram • written by engineer.khan • engineer.khan

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

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written by russhh russhh

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

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written by engineer.khan • engineer.khan

1 answer

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.

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updated by Ram Ram • written by Charles Warden Charles Warden

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

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written by engineer.khan • engineer.khan

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