The integrated showing error

[honghh2018]

Hi guy, When i runing on below step, adatas_cor = scanorama.correct_scanpy(adatas, return_dimred=True) It was complain about error: Error: No genes found in all datasets, exiting...

NameError Traceback (most recent call last) /tmp/ipykernel_146881/3261772617.py in ----> 1 adatas_cor = scanorama.correct_scanpy(adatas, return_dimred=True)

/share/nas1/Data/software/mini_conda/Miniconda3/envs/Scanpy_package/lib/python3.8/site-packages/scanorama/scanorama.py in correct_scanpy(adatas, **kwargs) 219 """ 220 if 'return_dimred' in kwargs and kwargs['return_dimred']: --> 221 datasets_dimred, datasets, genes = correct( 222 [adata.X for adata in adatas], 223 [adata.var_names.values for adata in adatas],

/share/nas1/Data/software/mini_conda/Miniconda3/envs/Scanpy_package/lib/python3.8/site-packages/scanorama/scanorama.py in correct(datasets_full, genes_list, return_dimred, batch_size, verbose, ds_names, dimred, approx, sigma, alpha, knn, return_dense, hvg, union, seed) 90 datasets_full = check_datasets(datasets_full) 91 ---> 92 datasets, genes = merge_datasets(datasets_full, genes_list, 93 ds_names=ds_names, union=union) 94 datasets_dimred, genes = process_data(datasets, genes, hvg=hvg,

/share/nas1/Data/software/mini_conda/Miniconda3/envs/Scanpy_package/lib/python3.8/site-packages/scanorama/scanorama.py in merge_datasets(datasets, genes, ds_names, verbose, union) 336 if len(keep_genes) == 0: 337 print('Error: No genes found in all datasets, exiting...') --> 338 exit(1) 339 if verbose: 340 print('Found {} genes among all datasets'

NameError: name 'exit' is not defined

So how can i fix this issue? Any advice would be appreciated

[brianhie]

Hi @honghh2018, could you make sure that the genes you are passing to scanorama are the same? By default, it will take the intersection of all gene sets.