Varm 'replaced' needs to be of one of np.ndarray

[CarrieChen0530]

Hello,
After reading your paper, I became very interested in Omicverse. After learning more about it, I found that Omicverse provides great convenience for data analysis. However, I encountered some issues when running the Differential Expression Analysis with DESeq2 code. When I input the following code:
treatment_groups = ['4-3', '4-4']
control_groups = ['1--1', '1--2']
result = dds.deg_analysis(treatment_groups, control_groups, method='DESeq2')

I received the following error:
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'>.

I then modified the code to:
treatment_groups = np.ndarray['4-3', '4-4']
control_groups = np.ndarray['1--1', '1--2']
result = dds.deg_analysis(treatment_groups, control_groups, method='DESeq2')

But I received this error:
TypeError: unsupported operand type(s) for +: 'types.GenericAlias' and 'types.GenericAlias'

I would appreciate your response. Thank you.

(Also, I don't quite understand the meaning of the hyphens in "4-3" and "1--1". I would appreciate your clarification as well. Thank you so much.)

[GhostInTheShellwjc]

Perhaps you can modify your numpy version to 1.26.4 and have a try.It goes well on my Jupyter
on vscode in Windows 11.
If you need version info about other packages,feel free to ask me at any time.

[CarrieChen0530]

It seems the issue isn't related to the version of NumPy since you're already using version 1.26.4, and the versions are consistent. Could you please suggest other possible solutions? Thank you.

[GhostInTheShellwjc]

@CarrieChen0530 python 3.10.15 pydeseq2 0.4.12 pandas 1.5.3？follow your codes in the first time