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Questions Arising from Using Scanpy for Data Input and scVI for Batch Effect Removal

Hello everyone,

Upon inputting my data using Scanpy and subsequently attempting to utilize scVI for batch effect removal, I encountered the following error:

ValueError: Making .obs["ID"] categorical failed. Expected categories: ['b10' 'b11' 'b12' 'b13' 'b14' 'b15' 'b16' 'b17' 'b18' 'b19' 'b20' 'b21' 'b23' 'b24' 'b25' 'b26' 'b27' 'b28' 'b29' 'b30' 'b31' 'b32' 'b33' 'b34' 'b35' 'b36' 'b37' 'b38' 'b39' 'b40' 'b41' 'b42' 'b43' 'b44' 'b7' 'b8' 'b9']. Received categories: Index(['b10', 'b11', 'b12', 'b13', 'b14', 'b15', 'b16', 'b17', 'b18', 'b19', 'b20', 'b21', 'b23', 'b24', 'b25', 'b26', 'b27', 'b28', 'b29', 'b30', 'b31', 'b32', 'b33', 'b34', 'b35', 'b36', 'b37', 'b38', 'b39', 'b40', 'b41', 'b42', 'b43', 'b44', 'b7', 'b8', 'b9'], dtype='object').

When I run:

scvi.model.SCVI.setup_anndata(adata, layer="counts", batch_key="ID",)

I input data use:

k16.obs['donor_id']='k16'

I am not sure where I made mistakes, and I hope you could offer me some thoughts on solving this problem.

single scanpy cell scvi

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