theislab / diffxpy

Differential expression analysis for single-cell RNA-seq data.
https://diffxpy.rtfd.io
BSD 3-Clause "New" or "Revised" License
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Fit model error in constraint_system_from_star #190

Open Hrovatin opened 3 years ago

Hrovatin commented 3 years ago

When passing dmat to fit.model it errors out as it expects to receive 2 variables from constraint_system_from_star, but constraint_system_from_star actually returns 4 variables.


  result=de.fit.model(
      data=adata,
      dmat_loc=dmat_loc,
      dmat_scale=pd.DataFrame(dmat_loc['Intercept']),
      constraints_loc=constraints_loc,
      size_factors=adata.obs.size_factors_sample
      )

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-43-9bfb9d252cd9> in <module>
      9 
     10 if True:
---> 11     result=de.fit.model(
     12         data=adata,
     13         dmat_loc=dmat_loc,

~/miniconda3/envs/rpy2_3/lib/python3.8/site-packages/diffxpy/fit/fit.py in model(data, 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, training_strategy, quick_scale, dtype, **kwargs)
    190     )
    191 
--> 192     design_loc, constraints_loc = constraint_system_from_star(
    193         dmat=dmat_loc,
    194         sample_description=sample_description,

ValueError: too many values to unpack (expected 2)
davidsebfischer commented 3 years ago

Should be fixed on dev? See also https://github.com/theislab/diffxpy/issues/182