Open hw-ju opened 1 year ago
In /notebooks/hlca_lung_gpu_analysis.ipynb, when run cell 19
/notebooks/hlca_lung_gpu_analysis.ipynb
%%time hvg = rapids_scanpy_funcs.highly_variable_genes(sparse_gpu_array, genes, n_top_genes=5000)
it raises error:
--------------------------------------------------------------------------- AttributeError Traceback (most recent call last) <timed exec> in <module> /workspace/notebooks/rapids_scanpy_funcs.py in highly_variable_genes(sparse_gpu_array, genes, n_top_genes) 801 mean = sparse_gpu_array.sum(axis=0).flatten() / n_cells 802 mean_sq = sparse_gpu_array.multiply(sparse_gpu_array).sum(axis=0).flatten() / n_cells --> 803 variable_genes = _cellranger_hvg(mean, mean_sq, genes, n_cells, n_top_genes) 804 805 return variable_genes /workspace/notebooks/rapids_scanpy_funcs.py in _cellranger_hvg(mean, mean_sq, genes, n_cells, n_top_genes) 750 df = pd.DataFrame() 751 # Note - can be replaced with cudf once 'cut' is added in 21.08 --> 752 df['genes'] = genes.to_numpy() 753 df['means'] = mean.tolist() 754 df['dispersions'] = dispersion.tolist() AttributeError: 'Series' object has no attribute 'to_numpy'
Could you fix the rapids_scanpy_funcs.highly_variable_genes?
rapids_scanpy_funcs.highly_variable_genes
In
/notebooks/hlca_lung_gpu_analysis.ipynb
, when run cell 19it raises error:
Could you fix the
rapids_scanpy_funcs.highly_variable_genes
?