What is the difference between tissue and tissue_general

[Alex2975]

Dear Authors,

Could you please share what is the difference between the tissue and tissue_general? Thank you very much.

[pablo-gar]

Hi @Alex2975,

See our schema document for specific definitions.

• tissue – original tissue annotation.
• tissue_general – high-level mapping of a tissue, e.g. "Heart" is the tissue_general of "Heart left ventricle" .

[Alex2975]

Got it, thank you very much, @pablo-gar .

[Alex2975]

@pablo-gar , would it be possible to extract both raw and normalized expressions to one h5ad file? Can I use the following code, so that I have both raw expression and normalized expression in one h5ad? Thank you again.

with cellxgene_census.open_soma(census_version = 'latest') as census: adata = cellxgene_census.get_anndata( census = census, organism = "Homo sapiens", obs_value_filter="disease == 'normal' and is_primary_data == True", X_name = 'normalized', X_name = 'raw' )

[pablo-gar]

Yes, you can use the X_layers argument

adata = cellxgene_census.get_anndata(..., X_name = "raw", X_layers=["normalized"])

[Alex2975]

Great, thank you so much, @pablo-gar .