Methylation data, normalized?

[YIGE LI]

Hello!

I have download 450K methylation data from Xena browser TCGA hub. I saw "wrangling: Level_3 data download from TCGA DCC, processed at UCSC into Xena repository" in this page , I wonder what is the " process"? In addition,  after reading some research articles, I was confused whether this methylation data to be normalized?

Regards,

Lee.

[Mary Goldman]

Hi Lee,

For this data, processing means that we converted it from a csv to a tsv and things like that. Nothing that affected the values of the data themselves.

We did not perform any additional normalization on this data. Since it appears that you are looking at the legacy TCGA data, I recommend looking at the legacy TCGA publications for any normalization performed. These will be publications before the PanCan Atlas publications in 2018. This page may be useful: https://gdc.cancer.gov/about-data/publications#/?groups=&years=&order=desc&q=tcga

Best,

Mary

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Mary Goldman (she/her), Design and Outreach Engineer

UCSC Xena

UC Santa Cruz Genomics Institute

Revealing life's code

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