Matching the file names with exposure file in TCGA

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3.4 years ago

nazaninhoseinkhan ▴ 530

Dear all,

I have downloaded the gene expression data for Bladder cancer from TCGA and I wanted to select some patients based on the information provided in exposure file.

Unfortunately the file names (FPKM or FPKM-UQ) does not match with the ids in exposure file.

I inspected the metadata file and could found the corresponding ids for only 25% of file names.

Could any one guide me to solve this problem?

Thank u in advance

Nazanin

FPKM exposure TCGA • 908 views

ADD COMMENT • link updated 20 months ago by Ram 44k • written 3.4 years ago by nazaninhoseinkhan ▴ 530

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I'm not familiar with this site, but the original publication(s) may have the info in supplementary, or you could use this and check if the data has been uploaded to another public repository such as GEO, and you may find the raw data and more metadata there.

ADD REPLY • link 3.4 years ago by biomon ▴ 60

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I could find the solution with "GenomicDataCommon" package and Manifest data

ADD REPLY • link 3.4 years ago by nazaninhoseinkhan ▴ 530

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