Filtering cells using scanpy
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16 months ago

I have to filter cells on basis of gene expression using scanpy. I am using the command

sc.pp.filter_cells(adata, min_genes=0)

But I am getting this error:

File "<stdin>", line 1, in <module> File "/storage/gaurav.ahuja/python2/envs/scenic/lib/python3.6/site-packages/scanpy/preprocessing/_simple.py", line 125, in filter_cells cell_subset, number = materialize_as_ndarray(filter_cells(adata.X, min_counts, min_genes, max_counts, max_genes)) File "/storage/gaurav.ahuja/python2/envs/scenic/lib/python3.6/site-packages/scanpy/preprocessing/_simple.py", line 136, in filter_cells else X > 0, axis=1) TypeError: '>' not supported between instances of 'numpy.ndarray' and 'int'

Before this step, I had just read the expression matrix and made the values unique using var_name_make_unique

Please suggest the solution.

python scanpy gene RNA-Seq sequencing • 616 views
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