PayneLab/cptac

inconsistent data with PDC

Closed this issue · 1 comments

sky1ove commented

Inconsistent data with PDC:

in this package, UCEC cancer has these tumor_and_normal data:

image

but in PDC, these data are defined as tumor only
image

The PDC meta file is downloaded from https://pdc.cancer.gov/pdc/cptac-pancancer, and under this file Proteome_Broad_Institute_harmonized_v1.tsv.gz

sabmel commented

Hello! Currently, we only use Umich and BCM as sources for proteomic data, not the Broad. In other words: Proteome_BCM_GENCODE_v34_harmonized_v1.zip and Proteome_UMich_GENCODE34_v1.zip