error in bulk deg part

[baconchan]

result=dds.deg_analysis(treatment_groups,control_groups,method='DEseq2',
multipletests_method=None)

Fitting size factors...
... done in 0.01 seconds.

Fitting dispersions...
... done in 29.57 seconds.

Fitting dispersion trend curve...
... done in 6.88 seconds.

Fitting MAP dispersions...
logres_prior=1.4874080250589685, sigma_prior=1.0924739582107421
... done in 35.02 seconds.

Fitting LFCs...
... done in 31.84 seconds.

---

ValueError Traceback (most recent call last)
Cell In[8], line 3
1 treatment_groups=['D1','D2','D3','D4']
2 control_groups=['C1','C2','C3','C4']
----> 3 result=dds.deg_analysis(treatment_groups,control_groups,method='DEseq2',
4 multipletests_method=None)

File ~/miniconda3/envs/omicverse2/lib/python3.10/site-packages/omicverse/bulk/_Deseq2.py:609, in pyDEG.deg_analysis(self, group1, group2, method, alpha, multipletests_method, n_cpus, cooks_filter, independent_filter)
606 dds.calculate_cooks()
607 if dds.refit_cooks:
608 # Replace outlier counts
--> 609 dds.refit()
610 stat_res = DeseqStats(dds, alpha=alpha, cooks_filter=cooks_filter, independent_filter=independent_filter)
611 stat_res.run_wald_test()

File ~/miniconda3/envs/omicverse2/lib/python3.10/site-packages/pydeseq2/dds.py:813, in DeseqDataSet.refit(self)
807 """Refit Cook outliers.
808
809 Replace values that are filtered out based on the Cooks distance with imputed
810 values, and then re-run the whole DESeq2 pipeline on replaced values.
811 """
812 # Replace outlier counts
--> 813 self._replace_outliers()
814 if not self.quiet:
815 print(
816 f"Refitting {sum(self.varm['replaced']) } outliers.\n", file=sys.stderr
817 )

File ~/miniconda3/envs/omicverse2/lib/python3.10/site-packages/pydeseq2/dds.py:903, in DeseqDataSet._replace_outliers(self)
894 n_or_more = (
895 self.obsm["design_matrix"][
896 self.obsm["design_matrix"].columns[-1]
897 ].value_counts()
898 >= self.min_replicates
899 )
901 if n_or_more.sum() == 0:
902 # No sample can be replaced. Set self.replaced to False and exit.
--> 903 self.varm["replaced"] = pd.Series(False, index=self.var_names)
904 return
906 replaceable = n_or_more[
907 self.obsm["design_matrix"][self.obsm["design_matrix"].columns[-1]]
908 ]

File ~/miniconda3/envs/omicverse2/lib/python3.10/site-packages/anndata/_core/aligned_mapping.py:216, in AlignedActual.setitem(self, key, value)
215 def setitem(self, key: str, value: Value):
--> 216 value = self._validate_value(value, key)
217 self._data[key] = value

File ~/miniconda3/envs/omicverse2/lib/python3.10/site-packages/anndata/_core/aligned_mapping.py:279, in AxisArraysBase._validate_value(self, val, key)
277 msg = "Index.equals and pd.testing.assert_index_equal disagree"
278 raise AssertionError(msg)
--> 279 return super()._validate_value(val, key)

File ~/miniconda3/envs/omicverse2/lib/python3.10/site-packages/anndata/_core/aligned_mapping.py:100, in AlignedMappingBase._validate_value(self, val, key)
97 raise ValueError(msg)
99 name = f"{self.attrname.title().rstrip('s')} {key!r}"
--> 100 return coerce_array(val, name=name, allow_df=self._allow_df)

File ~/miniconda3/envs/omicverse2/lib/python3.10/site-packages/anndata/_core/storage.py:104, in coerce_array(value, name, allow_df, allow_array_like)
102 if e is not None:
103 msg += " (Failed to convert it to an array, see above for details.)"
--> 104 raise ValueError(msg) from e

ValueError: Varm 'replaced' needs to be of one of np.ndarray, numpy.ma.core.MaskedArray, scipy.sparse.spmatrix, awkward.Array, h5py.Dataset, zarr.Array, zappy.base.ZappyArray, anndata.experimental.[CSC,CSR]Dataset, dask.array.Array, cupy.ndarray, or cupyx.scipy.sparse.spmatrix, not <class 'pandas.core.series.Series'>.

omicverse 1.6.7

[DBinary]

This bug has been reported here: #307

Starting from v0.10.9, anndata no longer supports pandas DataFrames or Series in varm fields.
Fortunately, PyDeseq2 has addressed this bug in v0.4.11. I recommend updating your PyDeseq2 to v0.4.11 to resolve this issue.

Best wishes,
Lei

[DBinary]

This bug has been fixed in the latest version of OmicVerse.