Scanpy: gene find with visualization functions but not with subsetting

[shendong124]

I am looking for the expression of 'NCAM1'. It works when I am plotting my data (umap, violin plot, matrix plot) but I cant find it in the adata.var and I am not able to subset adata for this particular gene while it is working with the other genes.

#what works:
marker_genes = ['NCAM1']
ax = sc.pl.violin(adata, marker_genes, groupby='timepoint')

# what doesnt work:
subset_NCAM = adata[:, 'NCAM1']

"None of [Index(['NCAM1'], dtype='object', name='index')] are in the [index]"

Versions:

1.4.4

[LuckyMD]

Hi @shendong124,

My guess is that 'NCAM1' is in your adata.raw.var_names but not in adata.var_names. Could it be that you have filtered your adata after assigning adata.raw? When you plot gene expression, adata.raw is used to plot expression values by default.

[shendong124]

This was very helpful! thank you!