KeyError: missing elements

[saezlab]

KeyError: missing elements

[dbdimitrov]

Hi,

Please check your variable names. The default resource in LIANA is gene symbols. You can see by the error message that no variable matches the resource.

Let me know if this doesn't work :)

[rr-Yiran]

Hi,

Please check your variable names. The default resource in LIANA is gene symbols. You can see by the error message that no variable matches the resource.

Let me know if this doesn't work :)

Hi! Thanks for replying. I have checked the name, seems they are all already the gene symbols. This is the mouse genes, wonder if this affects that? Thank you.

print(adata.var_names[:50]) # This will print the first 10 gene identifiers
Index(['Xkr4', 'Sox17', 'Rgs20', 'St18', 'Sntg1', 'Cpa6', 'Sulf1', 'Kcnb2',
'Rdh10', 'Gdap1', 'Pi15', 'Crispld1', 'Il17a', 'Khdc1a', 'Kcnq5',
'Ptpn18', 'Neurl3', 'Gm5099', 'Rnf149', 'Il1r2', 'Il1r1', 'Il18r1',
'Il18rap', 'Fhl2', 'Ecrg4', 'Col3a1', 'Col5a2', 'Slc40a1', 'Tmeff2',
'Cavin2', 'Stat4', 'Stk17b', 'Aox3', 'Cd28', 'Ctla4', 'Icos', 'Nrp2',
'Zdbf2', 'Adam23', 'Myl1', 'Erbb4', 'Ikzf2', 'Fn1', 'Mreg', 'Igfbp5',
'Cxcr2', 'Slc11a1', 'Des', 'Pax3', 'Gm29536'],
dtype='object')

[dbdimitrov]

Hi,

Then if you select the MouseConsensus resource it should work (via resource_name). 🙂

[dbdimitrov]

I will assume this worked out. Feel free to open new issues.