Open le-ander opened 4 years ago
I have just tried running a wald test with a directly provided patsy design matrix. When I specified the size_factors argument, I got the following error (because sample_information is no longer provided when dmat is provided directly)
de.test.wald( data = adata_sub[adata_sub.obs['louvain_separate_fine'] == i], dmat_loc = dmat, formula_scale="~1", coef_totest = ["C(treatment_chronic, levels=l_chr)[T.Chr]"], batch_size=(1e9,512), train_args={"nproc": 40}, size_factors="size_factors" )
--------------------------------------------------------------------------- AttributeError Traceback (most recent call last) <ipython-input-30-a1ad529c1918> in <module> 6 batch_size=(1e9,512), 7 train_args={"nproc": 40}, ----> 8 size_factors="size_factors" 9 ) ~/.local/lib/python3.7/site-packages/diffxpy/testing/tests.py in wald(data, factor_loc_totest, coef_to_test, formula_loc, formula_scale, as_numeric, init_a, init_b, gene_names, sample_description, dmat_loc, dmat_scale, constraints_loc, constraints_scale, noise_model, size_factors, batch_size, backend, train_args, training_strategy, quick_scale, dtype, **kwargs) 641 size_factors=size_factors, 642 data=data, --> 643 sample_description=sample_description 644 ) 645 ~/.local/lib/python3.7/site-packages/diffxpy/testing/utils.py in parse_size_factors(size_factors, data, sample_description) 89 size_factors = size_factors.values 90 elif isinstance(size_factors, str): ---> 91 assert size_factors in sample_description.columns, "" 92 size_factors = sample_description[size_factors].values 93 AttributeError: 'NoneType' object has no attribute 'columns'
I have just tried running a wald test with a directly provided patsy design matrix. When I specified the size_factors argument, I got the following error (because sample_information is no longer provided when dmat is provided directly)