Problems running scDALI-Het/Hom

[lucia-ramirez]

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!

[seanken]

Hey! Following up on this, I am having the same issue with scDALI-Het, it fails about half way through.