Question: Access of triple negative breast cancer datasets from GDC
0
gravatar for fawazfebin
16 months ago by
fawazfebin0
fawazfebin0 wrote:

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.

ADD COMMENTlink modified 16 months ago • written 16 months ago by fawazfebin0
1
gravatar for Kevin Blighe
16 months ago by
Kevin Blighe41k
Guy's Hospital, London
Kevin Blighe41k wrote:

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

ADD COMMENTlink written 16 months ago by Kevin Blighe41k

Thank you Kevin . I shall have a try.

ADD REPLYlink written 16 months ago by fawazfebin0
0
gravatar for fawazfebin
16 months ago by
fawazfebin0
fawazfebin0 wrote:

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 COMMENTlink written 16 months ago by fawazfebin0
1

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 REPLYlink written 16 months ago by Kevin Blighe41k
0
gravatar for fawazfebin
16 months ago by
fawazfebin0
fawazfebin0 wrote:

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

ADD COMMENTlink written 16 months ago by fawazfebin0
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