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If my count table include number more than int32 (2147483647), it will raise Erro as follows:
in DeseqDataSet.__init__(self, adata, counts, clinical, design_factors, ref_level, min_mu, min_disp, max_disp, refit_cooks, min_replicates, beta_tol, n_cpus, batch_size, joblib_verbosity)
193 self.__dict__.update(adata.__dict__)
194 elif counts is not None and clinical is not None:
195 # Test counts before going further
--> 196 test_valid_counts(counts)
197 super().__init__(X=counts.astype(int), obs=clinical)
198 else:
...
135 raise ValueError("The count matrix should only contain integers.")
136 if (counts < 0).any().any():
--> 137 raise ValueError("The count matrix should only contain non-negative values.")
ValueError: The count matrix should only contain non-negative values.
Expected behavior
A temporary solution is to zoom in data before creating dds, as follows:
if counts_df.max().max() > 2147483647:
times = counts_df.max().max() / 2147483647
divide = int(times) + 1
counts_df = counts_df / divide
The text was updated successfully, but these errors were encountered:
If my count table include number more than int32 (2147483647), it will raise Erro as follows:
Expected behavior
A temporary solution is to zoom in data before creating dds, as follows:
The text was updated successfully, but these errors were encountered: