search

cBioPortal / icebox

very low priority issues
0 stars 0 forks source link

Issue with survival months attributes in Clinical tab in Comparison #109

Open jjgao opened 4 years ago

jjgao commented 4 years ago

Since the survival months (e.g. OS_MONTHS) include both time of event (e.g. death) and time of last follow up, the current analysis is not proper. Here are the options to fix the problem.

Opt 1. Exclude the patients that were censored, ie. status that is not 1, and add a note Opt 2. Remove the survival months attributes from the Clinical tab and add a note Opt 3. Merge the Survival tab into Clinical tab

While Opt 3 might be the cleanest, it'll make survival analysis more hidden. Maybe we should go with Opt 1 or 2 for now. Thinking it a bit more, I would vote for Opt 1 (slightly over Opt 2) as it will make the analysis proper while keeping the attributes.

@cBioPortal/product

Sjoerd-van-Hagen commented 4 years ago

As an option 4, how about we take option 3 but leave the survival tab in its current spot as well? Having two ways of getting to the same survival plot is not a bad thing, is it?

schultzn commented 4 years ago

I like option 4.

On Aug 21, 2020, at 12:29 PM, Sjoerd-van-Hagen notifications@github.com wrote:

As an option 4, how about we take option 3 but leave the survival tab in its current spot as well? Having two ways of getting to the same survival plot is not a bad thing, is it?

— You are receiving this because you are on a team that was mentioned. Reply to this email directly, view it on GitHub https://github.com/cBioPortal/cbioportal/issues/7819#issuecomment-678379429, or unsubscribe https://github.com/notifications/unsubscribe-auth/AC2XPYD26W6AZPCPLJTZE43SB2OHZANCNFSM4QHOMTNQ.

jjgao commented 4 years ago

Option 4 sounds good if we can solve one last issue: how to calculate q-values? If we calculate q values based all rows in the table of Clinical tab, they are going to be different from the q values in the Survival tab (implemented cBioPortal/cbioportal#7805)...

stale[bot] commented 3 years ago

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.