Matching pancancer expression to metadata

[greenelab]

Matching pancancer expression to metadata

[gwaybio]

pancan_scaled_rnaseq.tsv.gz includes sample level information while tcga-clinical_data.tsv includes patient level information. The sample level information identifiers are much more descriptive than the patient level information.

Mapping between the two files can be done by subsetting TCGA barcodes. Info here: https://docs.gdc.cancer.gov/Encyclopedia/pages/TCGA_Barcode/

This file might also be helpful: https://github.com/greenelab/pancancer/blob/master/data/sample_freeze.tsv

[GlastonburyC]

Isn't it the opposite?
pancan_scaled_rnaseq.tsv.gz looks like this:

Where as the clinical data contains the full barcode.

[gwaybio]

in either direction, the mapping can be done the same way. I don't think i've used the portion_id column though. Is there a sample_id column or something similar?

[GlastonburyC]

This file: https://github.com/greenelab/pancancer/blob/master/data/sample_freeze.tsv
made it trivial. Thanks