I was working with methylation data stored in TCGA couple months ago, but now the site changed and the methylation data is gone. Do someone know how can I find this data again?
I got a bit worried as well but it seems it can be found in the "legacy archive" available at https://gdc-portal.nci.nih.gov/legacy-archive..
Really sh*y move to just scrap the old portal..
I had built something similar to this and worst case it will now all be useless.
Yeah, I just learned about this change as well. I haven't taken a look at the files available at GDC yet, but I find this change to be very short sighted. There are numerous tools that rely upon the format of the files that were present at the old website and now these tools might be useless or have to be rewritten. I always thought it would be easy for me to update the clinical data in OncoLnc if I needed to, now I have no idea how long it will take.
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What do you mean by stored in TCGA? You mean submitted your data on DCC !!! If your submitted data on DCC is not accessible, contacting DCC will solve your problem rather than asking in blog.
Or if you meant you are not able to access methylation data from TCGA. The TCGA has been moved to GDC portal and go through the procedure to access TCGA data from GDC,
https://gdc.nci.nih.gov/access-data/data-access-processes-and-tools
Access via GDC data Transfer tool,
https://gdc.nci.nih.gov/access-data/gdc-data-transfer-tool
Access via web portal,
https://gdc.nci.nih.gov/access-data/gdc-data-portal
Neither I could find the methylation data. They may update in future but you can always contact them, that will ease your problem.