Open uqnsarke opened 1 month ago
Hi @uqnsarke
Thanks for opening a bug report. Can you please elaborate? From this information it is very difficult to figure out what might be going wrong.
Best,
Seppe
Hi Seppe Thanks for responding. My question is, to run "run_cgs_models_mallet", do I need to use individual objects or a merged object?? Because my merged object isnt working. If I run with individual objects and merge them after cistopic_obj.add_LDA_model(model) step, then find_clusters( cistopicobj, target = 'cell', k = 10, res = [0.6, 1.2, 3], prefix = 'pycisTopic', scale = True, split_pattern = '-' ) doesn't work. Its showing following error: "ValueError: Input X contains NaN."
But my data doesn't have NaN as you can see from below:: After filtering cell names and NaN values, number of cell names: 76219 After filtering cell names and NaN values, cell data shape: (76219, 32)
Hi Seppe Thanks for responding. My question is, to run "run_cgs_models_mallet", do I need to use individual objects or a merged object?? Because my merged object isnt working. If I run with individual objects and merge them after cistopic_obj.add_LDA_model(model) step, then find_clusters( cistopicobj, target = 'cell', k = 10, res = [0.6, 1.2, 3], prefix = 'pycisTopic', scale = True, split_pattern = '-' ) doesn't work. Its showing follwoing error: "ValueError: Input X contains NaN."
But my data doesn't have NaN as you can see from below:: After filtering cell names and NaN values, number of cell names: 76219 After filtering cell names and NaN values, cell data shape: (76219, 32)
Hi @uqnsarke
You should run topic modelling after merging your objects.
What error are you getting with the merged object?
Best,
Seppe
model_results = run_cgs_models_mallet( cistopic_obj=cistopic_obj, n_topics=n_topics, n_cpu=n_cpu, n_iter=n_iter, random_state=random_state, alpha=alpha, alpha_by_topic=alpha_by_topic, eta=eta, eta_by_topic=eta_by_topic, tmp_path=tmp_path, mallet_path=mallet_path, save_path=out_dir )...not working with all samples , output is showing only one object info