Input X contains NaN.

[christophechu]

dyn.tl.cell_velocities(adata, method='kmc', other_kernels_dict={'transform': 'sqrt'})
raise 'Input X contains NaN.'

[Sichao25]

Hi, thanks for raising this issue. Basically, this error occurs when there are NaN values in your dataset (Could be either in expression or velocity matrix). Could you share additional details about your issue(e.g. the dataset you are working with, previous steps you've performed, relevant traceback ...)?

[christophechu]

It should by definition not have any NA value. But I don't know why this problem has arisen.

adata_raw = adata.copy()
preprocessor = dyn.pp.Preprocessor(cell_cycle_score_enable=True)
preprocessor.config_monocle_recipe(adata_raw)
preprocessor.filter_cells_by_outliers_kwargs["keep_filtered"] = False
preprocessor.filter_genes_by_outliers_kwargs["inplace"]=True
preprocessor.select_genes_kwargs["n_top_genes"]=3000
preprocessor.preprocess_adata_monocle(adata_raw)
adata = adata_raw.copy()
adata.raw = adata
del adata_raw

AnnData object with n_obs × n_vars = 150931 × 7305
obs: 'file_name', 'n_genes_by_counts', 'log1p_n_genes_by_counts', 'total_counts', 'log1p_total_counts', 'pct_counts_in_top_20_genes', 'total_counts_mt', 'log1p_total_counts_mt', 'pct_counts_mt', 'outlier_5', 'mt_outlier', 'scDblFinder_score', 'scDblFinder_class', 'hybrid_score', 'hybrid_class', 'DoubletFinder_score', 'DoubletFinder_class', 'n_genes', 'Doublet_detect', 'patient', 'tissue', 'dataset', 'nGenes', 'nCounts', 'pMito', 'pass_basic_filter', 'Size_Factor', 'initial_cell_size', 'unspliced_Size_Factor', 'initial_unspliced_cell_size', 'spliced_Size_Factor', 'initial_spliced_cell_size', 'ntr'
var: 'nCells', 'nCounts', 'pass_basic_filter', 'log_cv', 'log_m', 'score', 'frac', 'use_for_pca', 'ntr', 'use_for_dynamics'
uns: 'CD4_subtypes_colors', 'diffmap_evals', 'neighbors', 'pp', 'velocyto_SVR', 'feature_selection', 'PCs', 'explained_variance_ratio_', 'pca_mean', 'vel_params_names', 'dynamics'
obsm: 'X_diffmap', 'X_pca_harmony', 'X_umap', 'X_pca'
varm: 'vel_params'
layers: 'spliced', 'unspliced', 'X_unspliced', 'X_spliced', 'M_u', 'M_uu', 'M_s', 'M_us', 'M_ss', 'velocity_S'
obsp: 'connectivities', 'distances', 'moments_con'

[Sichao25]

Would you mind sharing the traceback information? This will help us better locate the error.