ValueError: Please check if appropriate organism/ID type was provided!

[anke-king]

I get this error and it lists a number of genes that are not found in the data, although they are in var names (I checked). So I have no idea why this error occurs?

Also im trying to assess communication between mouse and human cells, so what would I have to specify as organism?

Thanks for the help!

[dbdimitrov]

Hi @anke-king,

Can you please show the adata.var of your data and how do you specify the resource which liana is using (e.g. via resource_name)?

[anke-king]

I used the default, so not specifying anything (trying to follow your tutorial)
Here is a short subset of my var_names:

print(adata_human_mouse.var_names[adata_human_mouse.var_names.str.startswith("CCL")]):

Index(['CCL1', 'CCL11', 'CCL12', 'CCL15', 'CCL15-CCL14', 'CCL17', 'CCL22',
'CCL23', 'CCL24', 'CCL28', 'CCL3', 'CCL4', 'CCL4L2', 'CCL5', 'CCL7',
'CCL8'],
dtype='object')

some of these are required in the error message and said not to be in var_names although they are there?
Should I specify a different resource? I tried mouseconensus but the same error occurs (also all my gene names are in human format).

[dbdimitrov]

Hi @anke-king,

If you can share a subset of your data and the function you were using from liana, I can debug it on my end.

Daniel

[soniyalama]

You should add use_raw = False