I'm trying to add some clinical data to each of 75 individual samples (.obs) from bulk RNA sequencing. However, each individual sample can have 3-5 visits (treatments, etc) and I can't quite "expand" from 75 samples to 190+ samples as it throws an error, since the original adata is of size (75, 42000)
For example:
Say we have an ID called R1_70 and this ID (patient) had 5 visits and each visit has new information (Treatment type, visit date, etc). How can I add this and associate it with R1_70 on my .obs without expanding over the original size of 75 samples? One hot encoding wouldn't work here. Maybe if I "explode" each column to have "col_A_visit_1","col_B_visit_2", etc, but then this would make it quite awkward to run DEG, functional, analysis, etc with tools like scanpy or decoupler.
Hello
I'm trying to add some clinical data to each of 75 individual samples (.obs) from bulk RNA sequencing. However, each individual sample can have 3-5 visits (treatments, etc) and I can't quite "expand" from 75 samples to 190+ samples as it throws an error, since the original adata is of size (75, 42000)
For example:
Say we have an ID called R1_70 and this ID (patient) had 5 visits and each visit has new information (Treatment type, visit date, etc). How can I add this and associate it with R1_70 on my .obs without expanding over the original size of 75 samples? One hot encoding wouldn't work here. Maybe if I "explode" each column to have "col_A_visit_1","col_B_visit_2", etc, but then this would make it quite awkward to run DEG, functional, analysis, etc with tools like scanpy or decoupler.
Any help on how to do this is welcome!
Thanks