Dear Depmap team,
I have downloaded a version of PRISM Drug sensitivity AUC data in January 2021 (I suppose the version is newer than 19Q4). However recently when I check the Depmap portal I can’t find that version anymore and the newest version is only 19Q4. I’m quite sure that this is not the version I downloaded before because the one I downloaded has afatinib which is not in the 19Q4. Can I ask what happened with the version I downloaded before?
Thank you so much for your help!
This is a little puzzling because I believe the 19Q4 version is what would have been what you would have found on the portal if you downloaded the PRISM drug sensitivity data in Jan 2021.
Also, when you say afatinib is missing from 19Q4, which file specifically are you looking for it within?
If I look up afatinib on the portal, it reports that it was screened as part of the PRISM repurposing screen, but only the primary screen.
I downloaded secondary-screen-dose-response-curve-parameters.csv and I see afatinib there. So, there is potentially an issue where some secondary data is missing from the portal, but it appears to exist in the downloads.
Are you looking at secondary-screen-dose-response-curve-parameters.csv or somewhere else?
Thanks,
Phil
Dear Phil,
Thank you so much for your response.
I checked again and afatinib appear in the download but not portal. A few months ago I can still plot on the portal using afatinib data from the Drug sensitivity AUC dataset but now cannot. Is it a bug?
AN
Yes, I believe it is not appearing due to a bug. We have this logged in our issue tracker for someone to investigate more.
Thanks,
Phil
Dear Phil,
I cannot find the file secondary-screen-dose-response-curve-parameters.csv in the download section of the portal anymore. Is it has been removed? And I also cannot find afatinib in the file Drug_sensitivity_AUC_(PRISM_Repurposing_Secondary_Screen)_19Q4.csv.
Can you help me with this? Thank you so much.
No, it hasn’t been removed. I just looked it up and see it under the PRISM Repurposing 19Q4 release:
The other filename you mentioned looked like you maybe used the custom file export? If so, it’ll reflect what the portal shows. I’d recommend using the file I highlighted in the screenshot instead.
Let me know if you still have trouble locating it.
Thanks,
Phil
Dear Phil,
Thank you so much for your response. I have found the file.
In addition, I noticed that afatinib has 2 screenings with different broad_id (BRD-K66175015-001-09-0 and BRD-K66175015-001-12-4) and different screen_id (MTS010 and HTS002). The results of these 2 screenings are quite different, for example cell line CAL27 has lower AUC compared to HSC3 in HTS002, however, in the MTS010 screening, it is opposite. Can you explain what is the difference between the two screening and why the results are different?
Thank you!
Best regard,
Anh Nguyen
