[BUG] DeseqDataSet no types given
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Description
Describe the bug
A clear and concise description of what the bug is.
after uploaded the two type of files, i try to run dds = DeseqDataSet(
counts= counts_df,
clinical= clinical_df,
design_factors= ["condition", "group"],
refit_cooks=True,
n_cpus=8,
) but i get a ValueError: no types given.
As 'clinical_df =' Iused pd.read_excel (sample name, condition, group), while as 'counts_df =' I used pd.read_excel... .T (to traspose) (sample name x gene names) (i have 180 rows x 20365 columns).
I used the last version avilable 0.3.3
To Reproduce
dds = DeseqDataSet(
counts= counts_df,
clinical= clinical_df,
design_factors= ["condition", "group"],
refit_cooks=True,
n_cpus=8,
).
Expected behavior
A clear and concise description of what you expected to happen.
Screenshots

Desktop (please complete the following information):
- OS: [e.g. iOS]
- Version [e.g. 0.02]
Additional context
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Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start at the DeseqDataSet(...) entry point and inspect how the reported counts_df and clinical_df inputs are validated. Reproduce the constructor call with the two Excel-derived tables, then verify that the same inputs no longer raise the reported “no types given” ValueError.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100