f"Values {list(not_found)}, from {list(indexer)}, " "are not valid obs/ var names or indices."

[brianpenghe]

This bug only occurred in 1.6.0 but not 1.5.0

I was running scanpy 1.6.0 this:

sc.tl.filter_rank_genes_groups(adata, groupby=obs,\ max_out_group_fraction=max_out_group_fraction, min_fold_change=min_fold_change,use_raw=use_raw, min_in_group_fraction=0.25,log=log)

But got this error:

Filtering genes using: min_in_group_fraction: 0.25 min_fold_change: 2, max_out_group_fraction: 0.25

---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
<ipython-input-91-d477dca208af> in <module>
      2                     max_out_group_fraction=max_out_group_fraction,
      3                     min_fold_change=min_fold_change,use_raw=use_raw,
----> 4                     min_in_group_fraction=0.25,log=log)

/usr/local/lib/python3.6/dist-packages/scanpy/tools/_rank_genes_groups.py in filter_rank_genes_groups(adata, key, groupby, use_raw, log, key_added, min_in_group_fraction, min_fold_change, max_out_group_fraction)
    725             var_names,
    726             groupby='__is_in_cluster__',
--> 727             use_raw=use_raw,
    728         )
    729 

/usr/local/lib/python3.6/dist-packages/scanpy/plotting/_anndata.py in _prepare_dataframe(adata, var_names, groupby, use_raw, log, num_categories, layer, gene_symbols)
   1808         matrix = adata.raw[:, var_names].X
   1809     else:
-> 1810         matrix = adata[:, var_names].X
   1811 
   1812     if issparse(matrix):

/usr/local/lib/python3.6/dist-packages/anndata/_core/anndata.py in __getitem__(self, index)
   1085     def __getitem__(self, index: Index) -> "AnnData":
   1086         """Returns a sliced view of the object."""
-> 1087         oidx, vidx = self._normalize_indices(index)
   1088         return AnnData(self, oidx=oidx, vidx=vidx, asview=True)
   1089 

/usr/local/lib/python3.6/dist-packages/anndata/_core/anndata.py in _normalize_indices(self, index)
   1066 
   1067     def _normalize_indices(self, index: Optional[Index]) -> Tuple[slice, slice]:
-> 1068         return _normalize_indices(index, self.obs_names, self.var_names)
   1069 
   1070     # TODO: this is not quite complete...

/usr/local/lib/python3.6/dist-packages/anndata/_core/index.py in _normalize_indices(index, names0, names1)
     33     ax0, ax1 = unpack_index(index)
     34     ax0 = _normalize_index(ax0, names0)
---> 35     ax1 = _normalize_index(ax1, names1)
     36     return ax0, ax1
     37 

/usr/local/lib/python3.6/dist-packages/anndata/_core/index.py in _normalize_index(indexer, index)
     99                 not_found = indexer[positions < 0]
    100                 raise KeyError(
--> 101                     f"Values {list(not_found)}, from {list(indexer)}, "
    102                     "are not valid obs/ var names or indices."
    103                 )

KeyError: "Values ['LINC00601', 'DPYS', 'AC136604.2', 'AC023137.1', 'MATN3', 'AL359921.1' 
...
 'FAM129C', 'TCL1A'], are not valid obs/ var names or indices."

[LisaSikkema]

Hi Brian,
Did you do any subsetting of your adata between running rank_genes_groups and filter_rank_genes_groups? The only way I can reproduce your error is by removing genes from my adata in between the two commands.

[brianpenghe]

Hi Lisa, I didn't remove genes. Currently I'm using scanpy1.5.0 and everything is fine.

[LisaSikkema]

Okay, when I run this:
adata = sc.datasets.pbmc68k_reduced()
sc.tl.rank_genes_groups(adata, "bulk_labels", method="wilcoxon")
sc.tl.filter_rank_genes_groups(adata, min_fold_change=3)
I get no error.
Can you find a reproducible example of your error?

[jnmark]

@brianpenghe Did you find a solution for this? I am getting the same error in scanpy 1.7.0.