vitkl
commented
2 years ago Hi
This interface is deprecated. Please install latest version and follow the latest tutorial: https://cell2location.readthedocs.io/en/latest/notebooks/cell2location_tutorial.html
On Tue, 11 Jan 2022, 13:59 rue1996, @.***> wrote:
I am getting this error when i am running: training the model
Traceback (most recent call last): File "/scratch/ms/visium_08_10_21/brain_visium_data/Allen_brain/allen_convert.py", line 44, in r, adata_snrna_raw = run_regression(adata_snrna_raw, # input data object] File "/home/ms/.local/lib/python3.9/site-packages/cell2location/run_regression.py", line 144, in run_regression X_data = sc_data.raw.X.toarray() AttributeError: 'numpy.ndarray' object has no attribute 'toarray'
Not sure if it is still the issue that this only works with sparse.matrix and not numpy array?
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I am getting this error when i am running: training the model
Traceback (most recent call last): File "/scratch/ms/visium_08_10_21/brain_visium_data/Allen_brain/allen_convert.py", line 44, in
r, adata_snrna_raw = run_regression(adata_snrna_raw, # input data object]
File "/home/ms/.local/lib/python3.9/site-packages/cell2location/run_regression.py", line 144, in run_regression X_data = sc_data.raw.X.toarray()
AttributeError: 'numpy.ndarray' object has no attribute 'toarray'
Not sure if it is still the issue that this only works with sparse.matrix and not numpy array?