WeilerP
commented
11 months ago Cannot reproduce problem. From the looks of it, you stored entries as a Pandas DataFrame instead of numpy array or scipy sparse matrix.
Closed rohitarorayyc closed 11 months ago
WeilerP
commented
11 months ago Cannot reproduce problem. From the looks of it, you stored entries as a Pandas DataFrame instead of numpy array or scipy sparse matrix.
Issue when running filter_and_normalize ...
scv.pp.filter_and_normalize(adata, min_shared_counts=20, n_top_genes=2000) or from scvelo.core import get_initial_size, get_size, multiply, set_initial_size, sum set_initial_size(adata)
Error output
```pytb # paste the error output here, if applicable ``` AnnData object with n_obs × n_vars = 391167 × 36601 obs: 'barcode', 'Sex', 'Race', 'ABRH', 'donor_id', 'n_genes_by_counts', 'log1p_n_genes_by_counts', 'total_counts', 'log1p_total_counts', 'pct_counts_in_top_50_genes', 'pct_counts_in_top_100_genes', 'pct_counts_in_top_200_genes', 'pct_counts_in_top_500_genes', 'total_counts_mt', 'log1p_total_counts_mt', 'pct_counts_mt', 'total_counts_rb', 'log1p_total_counts_rb', 'pct_counts_rb', 'total_counts_hb', 'log1p_total_counts_hb', 'pct_counts_hb', 'leiden', 'sample', 'batch', 'leiden_res0.5', 'cluster_dummy', 'leiden_res0.3', 'barcode' var: 'Accession', 'Chromosome', 'End', 'Start', 'Strand' obsm: 'X_umap' layers: 'matrix', 'ambiguous', 'spliced', 'unspliced' Normalized count data: X, spliced, unspliced. computing neighbors --------------------------------------------------------------------------- AttributeError Traceback (most recent call last) [/tmp/ipykernel_2609/2796425568.py](https://vscode-remote+ssh-002dremote-002bcompute-002da-002d16-002d162.vscode-resource.vscode-cdn.net/tmp/ipykernel_2609/2796425568.py) in ?() ----> 1 set_initial_size(adata) [~/.conda/envs/scvelo_env/lib/python3.9/site-packages/scvelo/core/_anndata.py](https://vscode-remote+ssh-002dremote-002bcompute-002da-002d16-002d162.vscode-resource.vscode-cdn.net/n/scratch3/users/r/roa422/~/.conda/envs/scvelo_env/lib/python3.9/site-packages/scvelo/core/_anndata.py) in ?(adata, layers) 598 None 599 """ 600 if layers is None: 601 layers = ["unspliced", "spliced"] --> 602 verify_dtypes(adata) 603 layers = [ 604 layer 605 for layer in layers [~/.conda/envs/scvelo_env/lib/python3.9/site-packages/scvelo/core/_anndata.py](https://vscode-remote+ssh-002dremote-002bcompute-002da-002d16-002d162.vscode-resource.vscode-cdn.net/n/scratch3/users/r/roa422/~/.conda/envs/scvelo_env/lib/python3.9/site-packages/scvelo/core/_anndata.py) in ?(adata) 752 except IndexError: 753 logg.warn( 754 "The data might be corrupted. Please verify all annotation datatypes." 755 ) --> 756 adata.uns = uns [~/.conda/envs/scvelo_env/lib/python3.9/site-packages/anndata/_core/anndata.py](https://vscode-remote+ssh-002dremote-002bcompute-002da-002d16-002d162.vscode-resource.vscode-cdn.net/n/scratch3/users/r/roa422/~/.conda/envs/scvelo_env/lib/python3.9/site-packages/anndata/_core/anndata.py) in ?(self, index) 1166 def __getitem__(self, index: Index) -> AnnData: 1167 """Returns a sliced view of the object.""" ... 6202 ): 6203 return self[name] -> 6204 return object.__getattribute__(self, name) AttributeError: 'DataFrame' object has no attribute 'dtype' Output is truncated. View as a scrollable element or open in a text editor. Adjust cell output settings...Versions
on current GitHub version ```pytb # paste the ouput of scv.logging.print_versions() here ``` scvelo==0.3.0 scanpy==1.9.5 anndata==0.10.3 loompy==3.0.7 numpy==1.26.1 scipy==1.11.3 matplotlib==3.7.2 sklearn==1.1.3 pandas==2.1.1 Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process. ERROR: XMLRPC request failed [code: -32500] RuntimeError: PyPI no longer supports 'pip search' (or XML-RPC search). Please use https://pypi.org/search (via a browser) instead. See https://warehouse.pypa.io/api-reference/xml-rpc.html#deprecated-methods for more information.