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what does this warning message mean?

Open eesiribloom opened this issue 11 months ago • 0 comments

Im wondering what this warning means and if this is true, how best to interpret the results / can I still get something meaningful from this? I ran wgbstools with nanopore sequencing of cancer samples (n=20) and with three control samples from the methylation atlas (n=3)

wgbstools find_markers \
--betas ${output_dir}/*/*.beta \
--blocks_path ${blocks} \
--groups_file ${groups_file} \
--targets TUMOUR \
--background CONTROL \
--min_cpg 3 \
--header \
--threads $(nproc) \
--verbose \
--out_dir ${output_dir}
conda/envs/wgbs_tools/lib/python3.11/site-packages/scipy/stats/_axis_nan_policy.py:634: RuntimeWarning: Precision loss occurred in moment calculation due to catastrophic cancellation. This occurs when the data are nearly identical. Results may be unreliable.
  return result_to_tuple(hypotest_fun_out(*samples, **kwds), n_out)

eesiribloom avatar May 13 '25 14:05 eesiribloom