AttributeError: 'NoneType' object has no attribute 'shape' when running fitTPT about scicsr HOT 3 CLOSED

Hi,

Could you please check the anndata object has the 'isotype' column which you are using the group cells, and whether 'M' & 'G3' both exist in the AnnData.obs slot? Seems it thinks it can't find the column / cells with these states?

Joseph

from scicsr.

from scicsr.

Hi,

Apologies for the late response - were busy with some other projects. Without the data it would be difficult to diagnose the problem - I would guess most likely it is because with the grouping of cells imposed the program was left with no cells for certain groups. I would also like to add, if the idea here is to analyse dynamics of CSR between M and G3, there is little point in running the fitTPT function - the idea of the function is to ask, in a multi-state system, what the data say about the different possible paths that get you from the 'start' state to the 'end' state. Since in the IGH genomic locus between M and G3 there are no other isotypes in the middle (I assume you are working on human data), there is no other ways to go from M to G3 other than a direct jump! So TPT - if it had work - would simply tell you a 100% switch from M to G3 - not very useful I would say ...

I am closing this issue for now but if there are any other things I can help then please open a new issue.

Best wishes,
Joseph

from scicsr.