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This error does not occur when using dc.pp.pseudobulk().
Code:
>>> import pertpy as pt
>>> adata = pt.dt.zhang_2021()
>>> adata = adata[adata.obs["Origin"] == "t", :].copy()
>>> adata.layers["counts"] = adata.X.copy()
>>> ps = pt.tl.PseudobulkSpace()
>>> pdata = ps.compute(
... adata,
... target_col="Patient",
... groups_col="Cluster",
... layer_key="counts",
... mode="sum",
... )
>>> pds2 = pt.tl.PyDESeq2(pdata, design="~Efficacy+Treatment")
>>> res_df = pds2.compare_groups(
... pdata,
... column="Efficacy",
... baseline="SD",
... groups_to_compare=["PR", "PD"],
... )
Traceback:
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
res_df = pds2.compare_groups(
pdata,
...<2 lines>...
groups_to_compare=["PR", "PD"],
)
File "/Users/luisheinzlmeier/Desktop/Repos/pertpy/pertpy/tools/_differential_gene_expression/_base.py", line 903, in compare_groups
model.fit(**fit_kwargs)
~~~~~~~~~^^^^^^^^^^^^^^
File "/Users/luisheinzlmeier/Desktop/Repos/pertpy/pertpy/tools/_differential_gene_expression/_pydeseq2.py", line 62, in fit
dds = DeseqDataSet(
adata=adata_for_dds,
...<3 lines>...
**kwargs,
)
File "/Users/luisheinzlmeier/Library/Application Support/hatch/env/virtual/pertpy/RYWIBvOS/hatch-test.py3.14-stable/lib/python3.14/site-packages/pydeseq2/dds.py", line 302, in __init__
self.obsm["design_matrix"] = self.design
~~~~~~~~~^^^^^^^^^^^^^^^^^
File "/Users/luisheinzlmeier/Library/Application Support/hatch/env/virtual/pertpy/RYWIBvOS/hatch-test.py3.14-stable/lib/python3.14/site-packages/anndata/_core/aligned_mapping.py", line 219, in __setitem__
value = self._validate_value(value, key)
File "/Users/luisheinzlmeier/Library/Application Support/hatch/env/virtual/pertpy/RYWIBvOS/hatch-test.py3.14-stable/lib/python3.14/site-packages/anndata/_core/aligned_mapping.py", line 278, in _validate_value
raise ValueError(msg) from None
ValueError: value.index does not match parent’s obs names:
Index are different
Attribute "inferred_type" are different
[left]: empty
[right]: stringVersions
| Package | Version |
| ------- | ------- |
| pertpy | 1.1.0 |
| anndata | 0.12.16 |
| Dependency | Version |
| ------------------- | ---------------------- |
| jaxlib | 0.10.1 |
| interface_meta | 2.0.1 |
| ott-jax | 0.6.0 |
| llvmlite | 0.47.0 |
| fsspec | 2026.4.0 |
| cycler | 0.12.1 |
| h5py | 3.16.0 |
| asttokens | 3.0.1 |
| mudata | 0.3.8 |
| etils | 1.14.0 |
| scikit-learn | 1.8.0 |
| pure_eval | 0.2.3 |
| blitzgsea | 1.3.54 |
| packaging | 26.2 |
| jaxtyping | 0.3.10 |
| typing_extensions | 4.15.0 |
| fast-array-utils | 1.4.1 |
| comm | 0.2.3 |
| decorator | 5.3.1 |
| matplotlib | 3.10.9 |
| zarr | 3.2.1 |
| scverse-misc | 0.0.7 |
| numpyro | 0.21.0 |
| sparsecca | 0.3.1 |
| ml_dtypes | 0.5.4 |
| joblib | 1.5.3 |
| wrapt | 2.2.1 |
| donfig | 0.8.1.post1 |
| executing | 2.2.1 |
| multipledispatch | 1.0.0 (0.6.0) |
| adjustText | 1.3.0 |
| pyarrow | 24.0.0 |
| equinox | 0.13.8 |
| stack-data | 0.6.3 |
| pandas | 2.3.3 |
| jax | 0.10.1 |
| charset-normalizer | 3.4.7 |
| kiwisolver | 1.5.0 |
| wcwidth | 0.7.0 |
| legacy-api-wrap | 1.5 |
| parso | 0.8.7 |
| session-info2 | 0.4.1 |
| psutil | 7.2.2 |
| platformdirs | 4.10.0 |
| six | 1.17.0 |
| opt_einsum | 3.4.0 |
| pytz | 2026.2 |
| flax | 0.12.7 |
| seaborn | 0.13.2 |
| numpy | 2.4.6 |
| Pygments | 2.20.0 |
| patsy | 1.0.2 |
| filelock | 3.29.0 |
| tqdm | 4.67.3 |
| msgpack | 1.1.2 |
| threadpoolctl | 3.6.0 |
| pyparsing | 3.3.2 |
| optax | 0.2.8 |
| mpmath | 1.3.0 |
| absl-py | 2.4.0 |
| wadler_lindig | 0.1.7 |
| statsmodels | 0.14.6 |
| coverage | 7.14.1 |
| numba | 0.65.1 |
| lineax | 0.1.1 |
| jaxopt | 0.8.5 |
| setuptools | 81.0.0 |
| PubChemPy | 1.0.5 |
| google-crc32c | 1.8.0 |
| python-dateutil | 2.9.0.post0 |
| certifi | 2026.5.20 (2026.05.20) |
| rich | 15.0.0 |
| formulaic-contrasts | 1.0.0 |
| scikit-misc | 0.5.2 |
| pooch | 1.9.0 (v1.9.0) |
| jedi | 0.20.0 |
| PyYAML | 6.0.3 |
| pillow | 12.2.0 |
| formulaic | 1.2.1 |
| traitlets | 5.15.0 |
| natsort | 8.4.0 |
| scipy | 1.17.1 |
| scanpy | 1.12.1 |
| numcodecs | 0.16.5 |
| xarray | 2026.4.0 |
| ipython | 9.13.0 |
| prompt_toolkit | 3.0.52 |
| pydeseq2 | 0.5.4 |
| narwhals | 2.21.2 |
| ipywidgets | 8.1.8 |
| pyomo | 6.10.0 |
| Component | Info |
| --------- | ---------------------------------------------------------------------- |
| Python | 3.14.5 (main, May 10 2026, 10:21:34) [Clang 17.0.0 (clang-1700.6.4.2)] |
| OS | macOS-15.7.4-arm64-arm-64bit-Mach-O |
| Updated | 2026-06-01 06:20 |
Please make sure these conditions are met
Report
This error does not occur when using
dc.pp.pseudobulk().Code:
Traceback:
Versions