Question

Access of triple negative breast cancer datasets from GDC

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6.3 years ago

fawazfebin ▴ 100

Hi

I would like to dowload triple negative breast cancer data from GDC Data Portal. But I couldnt find data corresponding to this type of cancer . Can anyone help please? Thanks in advance.

triple negative breast cancer GDC • 2.5k views

ADD COMMENT • link 6.3 years ago by fawazfebin ▴ 100

score 1 · Answer 1 · 2017-12-15

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6.3 years ago

Kevin Blighe 87k

Look here: How to download triple negative breast cancer RNA-seq fpkm data from GDC.

ADD COMMENT • link 6.3 years ago by Kevin Blighe 87k

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Thank you Kevin . I shall have a try.

ADD REPLY • link 6.3 years ago by fawazfebin ▴ 100

score 0 · Answer 2 · 2017-12-19

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6.3 years ago

fawazfebin ▴ 100

Sorry Kevin. I couldn't find the 'er_status_by_ihc', 'pr_status_by_ihc', 'her2_status_by_ihc' columns in txt files you mentioned. What could be wrong? Thanks in advance.

ADD COMMENT • link 6.3 years ago by fawazfebin ▴ 100

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They are definitely there. er_status_by_ihc, for example, is in cell AR1.

This is the exact file: https://portal.gdc.cancer.gov/legacy-archive/files/735bc5ff-86d1-421a-8693-6e6f92055563

ADD REPLY • link 6.3 years ago by Kevin Blighe 87k

score 0 · Answer 3 · 2017-12-23

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6.3 years ago

fawazfebin ▴ 100

Yes Kevin, found the columns after downloading the file. Great thanks

ADD COMMENT • link 6.3 years ago by fawazfebin ▴ 100