Interpretation of TCGA clinical data

Question

[bxia]

When I parse the xml file from TCGA,

I saw something like "age_at_initial_diagnosis", 63, precision = day, then I check the TCGA website, it is 63 years old...

and there are several number in xml about last day follow up... which number is correct? some patients look like being followed for more than 1 times, but I did calculation...the number does not match...

Thanks

[jan]

Hi,

Can I just ask how did you parse the XML files ?

[Charles Warden]

Python has some XML (and JSON) libraries that can be imported, which you might find helpful:

https://docs.python.org/2/library/xml.etree.elementtree.html

https://docs.python.org/2/library/json.html

Answer 1

[Kristoffer Vitting-Seerup]

I would suggest to use the data provided by the TCGA CDR (Clinical Data Resource) which have been manually curated and concatenated. It is described in this paper and should solve many of those problems.

Answer 2

[igor]

I personally find that Xena is the easiest way to download TCGA-related data. All the datasets are aggregated in a basic table format with consistent sample names.

For example, the Pan-Cancer data is here: https://xenabrowser.net/datapages/?cohort=TCGA%20Pan-Cancer%20(PANCAN)&removeHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443