Problems running scDALI-Het/Hom #1
Description
Hello, I am trying to run scDALI on my data. I can run scDALI-Joint without any problems but when I try to run either scDALI-Het or scDALI-Hom I get some errors, even though is the same line of code (I only remove base_rate or cell_states depending on the mode).
This is the error that I get for scDALI-Het:
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
<ipython-input-48-8ea9456083cd> in <module>()
1 res = run_tests(A = A.transpose(),D = D.transpose() , model = 'scDALI-Het',
----> 2 cell_state = cell_states)
/software/teamtrynka/conda/sex_diff_upgrade/lib/python3.6/site-packages/scdali/run_scdali_tests.py in run_tests(A, D, model, X, cell_state, return_rho, base_rate, n_cores)
108 f,
109 mat_dict={'A':A, 'D':D},
--> 110 n_cores=n_cores)
111
112 out = dict()
/software/teamtrynka/conda/sex_diff_upgrade/lib/python3.6/site-packages/scdali/utils/parallel.py in process_parallel(fun_sequential, mat_dict, n_cores, verbose, show_progress)
53 if n_cores==1:
54 # don't invoke joblib
---> 55 results = fun_sequential(**mat_dict)
56 else:
57 blocks = np.linspace(0, n_cols, n_cores + 1).astype(int)
/software/teamtrynka/conda/sex_diff_upgrade/lib/python3.6/site-packages/scdali/utils/run_model.py in run_model(model, A, D, init_kwargs, fit_kwargs, callbacks, show_progress, verbose)
54
55 # fit model
---> 56 mod.fit(**fit_kwargs)
57
58 # run callbacks on fitted model
/software/teamtrynka/conda/sex_diff_upgrade/lib/python3.6/site-packages/scdali/models/glmm.py in fit(self, maxiter, tol)
127 if self.X is not None:
128 self.Lh = cho_factor(
--> 129 (self.W0 * self.X).T @ self.X + JITTER * np.eye(self.X.shape[1]))
130
131
/software/teamtrynka/conda/sex_diff_upgrade/lib/python3.6/site-packages/scipy/linalg/decomp_cholesky.py in cho_factor(a, lower, overwrite_a, check_finite)
151 """
152 c, lower = _cholesky(a, lower=lower, overwrite_a=overwrite_a, clean=False,
--> 153 check_finite=check_finite)
154 return c, lower
155
/software/teamtrynka/conda/sex_diff_upgrade/lib/python3.6/site-packages/scipy/linalg/decomp_cholesky.py in _cholesky(a, lower, overwrite_a, clean, check_finite)
25 if a1.shape[0] != a1.shape[1]:
26 raise ValueError('Input array is expected to be square but has '
---> 27 'the shape: {}.'.format(a1.shape))
28
29 # Quick return for square empty array
ValueError: Input array is expected to be square but has the shape: (8, 1).
And this is the error that I get with scDALI-Hom:
---------------------------------------------------------------------------
SystemExit Traceback (most recent call last)
<ipython-input-52-318a46fce7e4> in <module>()
----> 1 res = run_tests(A = A.transpose(),D = D.transpose() , model = 'scDALI-Hom', base_rate = 0.025)
/software/teamtrynka/conda/sex_diff_upgrade/lib/python3.6/site-packages/scdali/run_scdali_tests.py in run_tests(A, D, model, X, cell_state, return_rho, base_rate, n_cores)
108 f,
109 mat_dict={'A':A, 'D':D},
--> 110 n_cores=n_cores)
111
112 out = dict()
/software/teamtrynka/conda/sex_diff_upgrade/lib/python3.6/site-packages/scdali/utils/parallel.py in process_parallel(fun_sequential, mat_dict, n_cores, verbose, show_progress)
53 if n_cores==1:
54 # don't invoke joblib
---> 55 results = fun_sequential(**mat_dict)
56 else:
57 blocks = np.linspace(0, n_cols, n_cores + 1).astype(int)
/software/teamtrynka/conda/sex_diff_upgrade/lib/python3.6/site-packages/scdali/utils/run_model.py in run_model(model, A, D, init_kwargs, fit_kwargs, callbacks, show_progress, verbose)
59 region_results = list()
60 for cb in callbacks:
---> 61 region_results.append(cb(mod))
62 results.append(region_results)
63 return results
/software/teamtrynka/conda/sex_diff_upgrade/lib/python3.6/site-packages/scdali/utils/run_model.py in callback_method(model)
82 """
83 def callback_method(model):
---> 84 return getattr(model, method_name)(**kwargs)
85 return callback_method
86
/software/teamtrynka/conda/sex_diff_upgrade/lib/python3.6/site-packages/scdali/models/glmm.py in test(self, return_rho)
148 if len(self.rhos) == 1:
149 # approximate null distribution using Davies method
--> 150 pvalue = davies_pval(Q_rho[0], Fs[0])
151 if return_rho:
152 return pvalue, self.rhos[0]
/software/teamtrynka/conda/sex_diff_upgrade/lib/python3.6/site-packages/scdali/models/glmm.py in davies_pval(Q, F)
351 """Wrapper around davies_pvalue that catches AssertionError."""
352 try:
--> 353 pval = davies_pvalue(Q, F)
354 except AssertionError:
355 print('Warning - Davies pvalue assertion error: zero p-value')
/software/teamtrynka/conda/sex_diff_upgrade/lib/python3.6/site-packages/chiscore/_davies.py in davies_pvalue(q, w, return_info)
32 w = w / maxq
33
---> 34 re = _pvalue_lambda(_lambda(w), q)
35 if return_info:
36 return re["p_value"][0], re
/software/teamtrynka/conda/sex_diff_upgrade/lib/python3.6/site-packages/chiscore/_davies.py in _lambda(K)
102
103 if len(idx2) == 0:
--> 104 sys.exit("No Eigenvalue is bigger than 0!!")
105 return lambda1[idx2]
106
SystemExit: No Eigenvalue is bigger than 0!!
Thanks!