Skip to content

Why all genes showing NaN for the esmu score in one of the cell types on my end? #39

@noralis-bit

Description

@noralis-bit

here's the code:

adata = sc.read_h5ad("xxxxx")

ctype = "XXXX"
adata_subset = adata [adata .obs.ctype== ctype].copy()
counts_data = pd.DataFrame(adata_subset.X.toarray() ,index= adata_subset.obs_names, columns = adata_subset.var_names).T.rename_axis('gene', inplace=False)
metadata_sub = adata_subset.obs[["celltypes"]]

eso = cellex.ESObject(data=counts_data, annotation=metadata_sub, verbose=False)
eso.compute(verbose=False)    

image

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type
    No fields configured for issues without a type.

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions