ValueError: Length of values (1) does not match length of index with sc.pp.calculate_qc_metrics(adata)

• I have checked that this issue has not already been reported.
• I have confirmed this bug exists on the latest version of scanpy.
• (optional) I have confirmed this bug exists on the master branch of scanpy.

---

I also tried ‘log1p = False’ and produced the other error. Thank you.

sc.pp.calculate_qc_metrics(adata)

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/root/miniconda3/envs/scanpy/lib/python3.9/site-packages/scanpy/preprocessing/_qc.py", line 294, in calculate_qc_metrics
    obs_metrics = describe_obs(
  File "/root/miniconda3/envs/scanpy/lib/python3.9/site-packages/scanpy/preprocessing/_qc.py", line 111, in describe_obs
    obs_metrics[f"log1p_total_{expr_type}"] = np.log1p(
  File "/root/miniconda3/envs/scanpy/lib/python3.9/site-packages/pandas/core/frame.py", line 3612, in __setitem__
    self._set_item(key, value)
  File "/root/miniconda3/envs/scanpy/lib/python3.9/site-packages/pandas/core/frame.py", line 3784, in _set_item
    value = self._sanitize_column(value)
  File "/root/miniconda3/envs/scanpy/lib/python3.9/site-packages/pandas/core/frame.py", line 4509, in _sanitize_column
    com.require_length_match(value, self.index)
  File "/root/miniconda3/envs/scanpy/lib/python3.9/site-packages/pandas/core/common.py", line 531, in require_length_match
    raise ValueError(
ValueError: Length of values (1) does not match length of index (35255)
>

sc.pp.calculate_qc_metrics(adata, log1p = False)

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/root/miniconda3/envs/scanpy/lib/python3.9/site-packages/pandas/core/frame.py", line 995, in __repr__
    self.to_string(
  File "/root/miniconda3/envs/scanpy/lib/python3.9/site-packages/pandas/core/frame.py", line 1131, in to_string
    return fmt.DataFrameRenderer(formatter).to_string(
  File "/root/miniconda3/envs/scanpy/lib/python3.9/site-packages/pandas/io/formats/format.py", line 1053, in to_string
    string = string_formatter.to_string()
  File "/root/miniconda3/envs/scanpy/lib/python3.9/site-packages/pandas/io/formats/string.py", line 25, in to_string
    text = self._get_string_representation()
  File "/root/miniconda3/envs/scanpy/lib/python3.9/site-packages/pandas/io/formats/string.py", line 40, in _get_string_representation
    strcols = self._get_strcols()
  File "/root/miniconda3/envs/scanpy/lib/python3.9/site-packages/pandas/io/formats/string.py", line 31, in _get_strcols
    strcols = self.fmt.get_strcols()
  File "/root/miniconda3/envs/scanpy/lib/python3.9/site-packages/pandas/io/formats/format.py", line 540, in get_strcols
    strcols = self._get_strcols_without_index()
  File "/root/miniconda3/envs/scanpy/lib/python3.9/site-packages/pandas/io/formats/format.py", line 804, in _get_strcols_without_index
    fmt_values = self.format_col(i)
  File "/root/miniconda3/envs/scanpy/lib/python3.9/site-packages/pandas/io/formats/format.py", line 818, in format_col
    return format_array(
  File "/root/miniconda3/envs/scanpy/lib/python3.9/site-packages/pandas/io/formats/format.py", line 1240, in format_array
    return fmt_obj.get_result()
  File "/root/miniconda3/envs/scanpy/lib/python3.9/site-packages/pandas/io/formats/format.py", line 1271, in get_result
    fmt_values = self._format_strings()
  File "/root/miniconda3/envs/scanpy/lib/python3.9/site-packages/pandas/io/formats/format.py", line 1518, in _format_strings
    return list(self.get_result_as_array())
  File "/root/miniconda3/envs/scanpy/lib/python3.9/site-packages/pandas/io/formats/format.py", line 1482, in get_result_as_array
    formatted_values = format_values_with(float_format)
  File "/root/miniconda3/envs/scanpy/lib/python3.9/site-packages/pandas/io/formats/format.py", line 1456, in format_values_with
    values = format_with_na_rep(values, formatter, na_rep)
  File "/root/miniconda3/envs/scanpy/lib/python3.9/site-packages/pandas/io/formats/format.py", line 1427, in format_with_na_rep
    [
  File "/root/miniconda3/envs/scanpy/lib/python3.9/site-packages/pandas/io/formats/format.py", line 1428, in <listcomp>
    formatter(val) if not m else na_rep
ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()

Versions

WARNING: If you miss a compact list, please try print_header!

anndata 0.7.6 scanpy 1.7.2 sinfo 0.3.1

PIL 8.3.2 anndata 0.7.6 beta_ufunc NA binom_ufunc NA cffi 1.14.6 colorama 0.4.4 concurrent NA cycler 0.10.0 cython_runtime NA dateutil 2.8.2 dunamai 1.6.0 encodings NA genericpath NA get_version 3.5 h5py 3.4.0 joblib 1.0.1 kiwisolver 1.3.2 legacy_api_wrap 0.0.0 llvmlite 0.37.0 matplotlib 3.4.3 mpl_toolkits NA natsort 7.1.1 nbinom_ufunc NA ntpath NA numba 0.54.0 numexpr 2.7.3 numpy 1.20.3 opcode NA packaging 21.0 pandas 1.3.3 pkg_resources NA posixpath NA pycparser 2.20 pyexpat NA pyparsing 2.4.7 pytz 2021.1 scanpy 1.7.2 scipy 1.7.1 setuptools_scm NA sinfo 0.3.1 six 1.16.0 sklearn 1.0 sphinxcontrib NA sre_compile NA sre_constants NA sre_parse NA tables 3.6.1

Python 3.9.7 | packaged by conda-forge | (default, Sep 29 2021, 19:20:46) [GCC 9.4.0] Linux-5.4.72-microsoft-standard-WSL2-x86_64-with-glibc2.31 24 logical CPU cores, x86_64

Session information updated at 2021-10-01 14:56

[sfortma2]

Many thanks for everyone’s input. The bug is indeed due to an issue with Pandas ≥1.3. I am running Scanpy 1.8.1 and I can confirm that the indexing problem remains with Pandas 1.3.0, 1.3.2, and the latest 1.3.4, but resolves when downgrading to 1.2.5

[ivirshup]

My PR was merged, so this should be resolved with the next version of pandas.