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
In a somewhat related question, I was trying to download protein_quant_current_normalized.csv from the “All Data Downloads” page.
When I press the download file icon, it directs me to [Gygi Lab @ HMS] website without downloading the csv file.
From the customized download page, I have been able to download the following:
Harmonized_MS_CCLE_Gygi_subsetted.csv
Harmonized_RPPA_CCLE_subsetted.csv
Is protein_quant_current_normalized.csv equivalent to Harmonized_MS_CCLE_Gygi_subsetted.csv + Harmonized_RPPA_CCLE_subsetted.csv?
Thanks for you attention. Konrad
