Hey, I was trying to download proteome data on the portal, but the matrix I got was absent of any protein quantity. I am pretty sure I’ve downloaded proteome data of Gigi’s lab from Depmap before. Not sure if this is a glitch in the system. Your help would be appreciated.
Are you trying to use the “Custom downloads” tool to download a subset of the data by providing a list of genes?
I just tried the custom downloads UI and it appeared to successfully fetch the full dataset. However, specifying a single gene resulted in an empty file. I believe this is because this dataset is indexed by proteins as opposed to genes. (I notice the header from the full export has names like “AACS (Q86V21)”)
The custom downloads tool isn’t doesn’t have any logic in it to map proteins to genes before subsetting, so if one requests data for specific genes, it’ll just report an empty file.
If my guess is correct and you are trying to download a subset, I can see the confusion. ( At the very least, we should probably fix the UI to make it clear that filtering by gene will only work with a those datasets which are indexed by gene. )
Can you confirm that you’re able the download the file without subsetting?
Thanks,
Phil
