AttributeError: 'Liger' object has no attribute 'var_genes'

[mumichae]

I'm getting the following error when trying to run the scale_not_center function

Traceback (most recent call last):
File "/tmp/viash-run-pyliger-hnRbbi.py", line 45, in
pyliger.scale_not_center(lobj)
File "/usr/local/lib/python3.10/site-packages/pyliger/preprocessing/_scale.py", line 47, in scale_not_center
var_gene_idx = adata.var.index.isin(liger_object.var_genes)
AttributeError: 'Liger' object has no attribute 'var_genes'. Did you mean: 'num_var_genes'?

[theAeon]

Did you run select_genes on this object yet?

[mumichae]

No I hadn't, since I'm already working on a HVG subset that I want to be consistent across methods. Is there a way to run select_genes without recomputing HVGs?

[Lulu0015]

I think the issue is because we save a copy of HVGs during select_genes which will be used as a reference during the scale_not_center step. Can you try assigning your list of HVG to the Liger object attribute 'var_genes' to see if it fixes the issue? You may do things like liger_object.var_genes = YOU_LIST_HVG before running scale_not_center.