could not convert integer scalar

[brianpenghe]

adata=adata[:,~mito_genes]
I was running

sc.pp.filter_cells(adata, min_genes=200)

And got this error:

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-16-bc34931b4970> in <module>
----> 1 sc.pp.filter_cells(adata, min_genes=200)
      2 sc.pp.filter_genes(adata, min_cells=3)

/usr/local/lib/python3.6/dist-packages/scanpy/preprocessing/_simple.py in filter_cells(data, min_counts, min_genes, max_counts, max_genes, inplace, copy)
    123     if isinstance(data, AnnData):
    124         adata = data.copy() if copy else data
--> 125         cell_subset, number = materialize_as_ndarray(filter_cells(adata.X, min_counts, min_genes, max_counts, max_genes))
    126         if not inplace:
    127             return cell_subset, number

/usr/local/lib/python3.6/dist-packages/anndata/_core/anndata.py in X(self)
    577         elif self.is_view:
    578             X = as_view(
--> 579                 _subset(self._adata_ref.X, (self._oidx, self._vidx)),
    580                 ViewArgs(self, "X"),
    581             )

/usr/lib/python3.6/functools.py in wrapper(*args, **kw)
    805                             '1 positional argument')
    806 
--> 807         return dispatch(args[0].__class__)(*args, **kw)
    808 
    809     funcname = getattr(func, '__name__', 'singledispatch function')

/usr/local/lib/python3.6/dist-packages/anndata/_core/index.py in _subset(a, subset_idx)
    124     if all(isinstance(x, cabc.Iterable) for x in subset_idx):
    125         subset_idx = np.ix_(*subset_idx)
--> 126     return a[subset_idx]
    127 
    128 

/usr/local/lib/python3.6/dist-packages/scipy/sparse/_index.py in __getitem__(self, key)
     73         if row.size == 0:
     74             return self.__class__(np.atleast_2d(row).shape, dtype=self.dtype)
---> 75         return self._get_arrayXarray(row, col)
     76 
     77     def __setitem__(self, key, x):

/usr/local/lib/python3.6/dist-packages/scipy/sparse/compressed.py in _get_arrayXarray(self, row, col)
    663         val = np.empty(major.size, dtype=self.dtype)
    664         csr_sample_values(M, N, self.indptr, self.indices, self.data,
--> 665                           major.size, major.ravel(), minor.ravel(), val)
    666         if major.ndim == 1:
    667             return asmatrix(val)

ValueError: could not convert integer scalar

Any ideas?

[ivirshup]

Not sure. Could you follow up with these?

• Software versions for scanpy, anndata, scipy, and numpy
• type(adata) and type(adata.X)

Also, does it work if you do:

adata = adata.copy()
sc.pp.filter_cells(adata, min_genes=200)

[brianpenghe]

Not sure. Could you follow up with these?

• Software versions for scanpy, anndata, scipy, and numpy
• type(adata) and type(adata.X)

Also, does it work if you do:

adata = adata.copy()
sc.pp.filter_cells(adata, min_genes=200)

.copy()
worked!

[abuchin]

I have the same problem, but when I run

adata = adata.copy()

it shows the same problem:

...
~/anaconda2/envs/p7/lib/python3.7/site-packages/scipy-1.4.1-py3.7-macosx-10.9-x86_64.egg/scipy/sparse/compressed.py in _get_arrayXarray(self, row, col)
    663         val = np.empty(major.size, dtype=self.dtype)
    664         csr_sample_values(M, N, self.indptr, self.indices, self.data,
--> 665                           major.size, major.ravel(), minor.ravel(), val)
    666         if major.ndim == 1:
    667             return asmatrix(val)

ValueError: could not convert integer scalar

scanpy: 1.4.7.dev63+g0a6bf5ac
anndata: Version('0.7.1')
scipy: 1.4.1
numpy: 1.18.4

[abuchin]

Somehow the problem got solved when I updated these libraries.

[ivirshup]

Thanks for letting us know!