Key Error "base" in section "marker genes & annotation"

[Mari123i]

Hello Malte,
I get the following issue in the Marker genes section:
This is my AnnData Object:

And this is the error I get:

I work with the tutorial dataset in case it is relevant, but had to skip few steps containing R code.

Greetings,
Mariam

Edit:
The adata.uns["log1p"] seems to be empty

[LuckyMD]

Hi @Mari123i,

Did you run sc.pp.log1p on the data at some point? Then this slot should exist. Also, which version of scanpy are you using?

[Mari123i]

Hello,
Yes. I use 1.9.1. Its seems to be an error of saving it and loading it again

[LuckyMD]

This seems to be a scanpy bug as you can see here and here. The latter issue suggests to just add the line:

adata.uns['log1p']["base"] = None after reading again, or downgrading to AnnData<0.8. Either way, this should be fixed soon by the maintenance team.

[Mari123i]

It works! Thank you alot!