Hi, thanks for the tool.
When I try to run the tutorial or the figure note books (3 of them), I got the similar error: ValueError: setting an array element with a sequence.
For example: when try Pancreas dataset - complete pipeline:
### recover dynamics for all genes
velocity.tl.fit.recover_reaction_rate_pars(adata, use_raw=False, n=100,
fit_kappa=True, fit_scaling=True)
this line of code, raises error:
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
Cell In[14], line 2
1 ### recover dynamics for all genes
----> 2 velocity.tl.fit.recover_reaction_rate_pars(adata, use_raw=False, n=100,
3 fit_kappa=True, fit_scaling=True)
File ~/sw/velocity_package/velocity/tools/fit.py:10, in recover_reaction_rate_pars(adata, use_raw, n, key, fit_scaling, parallel, n_cores, n_parts, inplace, fit_kappa)
8 unspliced, spliced = adata.layers["unspliced" if use_raw else "Mu"], adata.layers["spliced" if use_raw else "Ms"]
9 if parallel:
---> 10 alpha, beta, gamma, U_switch, scaling, likelihood, Pi = fit_all_parallel(unspliced, spliced, n=n,
11 n_cores=n_cores, n_parts=n_parts,
12 fit_scaling=fit_scaling,
13 fit_kappa=fit_kappa)
14 else:
15 alpha, beta, gamma, U_switch, scaling, likelihood, Pi = fit_all(unspliced, spliced, n=n,
16 fit_scaling=fit_scaling, fit_kappa=fit_kappa)
File ~/sw/velocity_package/velocity/tools/fit.py:88, in fit_all_parallel(unspliced, spliced, n, n_cores, n_parts, fit_scaling, fit_kappa)
86 for i in result:
87 r.extend(i)
---> 88 r = np.array(r)
90 alpha, beta, gamma, U_switch, scaling, likelihood = r[:, 0], r[:, 1], r[:, 2], r[:, 3], r[:, 4], r[:, 5]
91 Pi = np.stack(r[:, 6]).T
ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 2 dimensions. The detected shape was (406, 7) + inhomogeneous part.
Hi, thanks for the tool. When I try to run the tutorial or the figure note books (3 of them), I got the similar error:
ValueError: setting an array element with a sequence.
For example: when try Pancreas dataset - complete pipeline:this line of code, raises error: