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Provide note to users for too many missing values in imputation #145

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Provide note to users for too many missing values in imputation #145

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54ce508
add grouping functionality to impute_gaussian and adapt/harmonize tes…
vbrennsteiner Dec 12, 2025
9bd8397
Merge branch 'main' into improve_impute_gaussian
vbrennsteiner Dec 13, 2025
6c933e0
update notebooks
vbrennsteiner Dec 30, 2025
290095c
refactoring of helper methods and adding additional bypass checks to …
vbrennsteiner Dec 30, 2025
042ec3b
adjust defaults to match between impute.py and test_impute.py
vbrennsteiner Dec 30, 2025
4702f98
add functions to warn if too many features are missing for imputation
vbrennsteiner Jan 12, 2026
643d8a1
add excessive missingness check to imputation methods
vbrennsteiner Jan 12, 2026
208bd09
add excessive missingness check to imputation methods
vbrennsteiner Jan 12, 2026
557a95b
reconcile differences between improve_gaussian_imputation and warn_to…
vbrennsteiner Jan 12, 2026
16d9e80
reconcile differences between improve_gaussian_imputation and warn_to…
vbrennsteiner Jan 12, 2026
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8 changes: 4 additions & 4 deletions docs/notebooks/04_differential_expression.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -63,7 +63,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
"/var/folders/2l/hhd_z4hx3070zw8rlj4c3l940000gn/T/tmp5j3sii7k/report.parquet does not yet exist\n"
"/var/folders/2l/hhd_z4hx3070zw8rlj4c3l940000gn/T/tmp2016cn1_/report.parquet does not yet exist\n"
]
},
{
Expand All @@ -77,8 +77,8 @@
"name": "stdout",
"output_type": "stream",
"text": [
"/var/folders/2l/hhd_z4hx3070zw8rlj4c3l940000gn/T/tmp5j3sii7k/report.parquet successfully downloaded (70.8467435836792 MB)\n",
"/var/folders/2l/hhd_z4hx3070zw8rlj4c3l940000gn/T/tmpr1853dya/iteration_L_literature_reprocessing_PELSA_samplemap.csv does not yet exist\n"
"/var/folders/2l/hhd_z4hx3070zw8rlj4c3l940000gn/T/tmp2016cn1_/report.parquet successfully downloaded (70.8467435836792 MB)\n",
"/var/folders/2l/hhd_z4hx3070zw8rlj4c3l940000gn/T/tmp2nq17bfx/iteration_L_literature_reprocessing_PELSA_samplemap.csv does not yet exist\n"
]
},
{
Expand All @@ -92,7 +92,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
"/var/folders/2l/hhd_z4hx3070zw8rlj4c3l940000gn/T/tmpr1853dya/iteration_L_literature_reprocessing_PELSA_samplemap.csv successfully downloaded (0.000179290771484375 MB)\n"
"/var/folders/2l/hhd_z4hx3070zw8rlj4c3l940000gn/T/tmp2nq17bfx/iteration_L_literature_reprocessing_PELSA_samplemap.csv successfully downloaded (0.000179290771484375 MB)\n"
]
}
],
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