Some of the proteomics data are not in the same format
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LifeWorks commented
endometrial has single level index, while ccrcc and brca have two levels of indices.
caleb-lindgren commented
That is intentional. In endometrial the original research team binned together all isoforms for a protein, while in ccrcc and brca they kept track of different isoforms. The second index level in those tables is a database ID that identifies the specific isoform.