diff --git a/paper-releases/20260928/diffusion/data/source_provenance/giroux2022/pairing/PAIRING_SUMMARY.json b/paper-releases/20260928/diffusion/data/source_provenance/giroux2022/pairing/PAIRING_SUMMARY.json new file mode 100644 index 0000000000000000000000000000000000000000..c0e3d28e0e5c033613b57a1ef032cf1ea5880d3f --- /dev/null +++ b/paper-releases/20260928/diffusion/data/source_provenance/giroux2022/pairing/PAIRING_SUMMARY.json @@ -0,0 +1,171 @@ +{ + "bulk_gsms": 71, + "bulk_subjects_geo": 29, + "bulk_count_table_columns": 49, + "bulk_count_table_subjects": 22, + "bulk_columns_matched_to_GSM": 43, + "bulk_columns_without_GSM": [ + "77DA77", + "22CBD6", + "4F2EAD", + "F8FF1A", + "56E219", + "3F05F3-14" + ], + "bulk_GSMs_without_count_column": 28, + "bulk_GSMs_without_count_column_by_group": { + "exposed": 20, + "healthy": 5, + "mild": 2, + "severe": 1 + }, + "sc_gsms": 41, + "sc_subjects": 18, + "geo_level_subject_day_matches": 39, + "geo_level_subject_day_matches_by_group": { + "mild": 15, + "severe": 13, + "exposed": 6, + "healthy": 5 + }, + "geo_level_subjects": 18, + "pairs_total": 26, + "pairs_subjects": 10, + "pairs_by_group": { + "mild": 13, + "severe": 13 + }, + "pairs_by_day": { + "0": 10, + "14": 9, + "7": 7 + }, + "sc_by_pair_status": { + "paired": 26, + "bulk_GSM_has_no_column_in_author_count_table": 13, + "no_bulk_GSM_for_this_subject_day": 2 + }, + "sc_unpaired": [ + { + "sc_gsm": "GSM6249237", + "sample_id": "450905_d7", + "group": "mild", + "pair_status": "bulk_GSM_has_no_column_in_author_count_table" + }, + { + "sc_gsm": "GSM6249239", + "sample_id": "7768E4_d2", + "group": "exposed", + "pair_status": "no_bulk_GSM_for_this_subject_day" + }, + { + "sc_gsm": "GSM6249240", + "sample_id": "7768E4_d14", + "group": "exposed", + "pair_status": "bulk_GSM_has_no_column_in_author_count_table" + }, + { + "sc_gsm": "GSM6249241", + "sample_id": "7768E4_d28", + "group": "exposed", + "pair_status": "no_bulk_GSM_for_this_subject_day" + }, + { + "sc_gsm": "GSM6249243", + "sample_id": "0B943B_d3", + "group": "mild", + "pair_status": "bulk_GSM_has_no_column_in_author_count_table" + }, + { + "sc_gsm": "GSM6249262", + "sample_id": "61BBAD_d0", + "group": "exposed", + "pair_status": "bulk_GSM_has_no_column_in_author_count_table" + }, + { + "sc_gsm": "GSM6249263", + "sample_id": "61BBAD_d7", + "group": "exposed", + "pair_status": "bulk_GSM_has_no_column_in_author_count_table" + }, + { + "sc_gsm": "GSM6249264", + "sample_id": "61BBAD_d14", + "group": "exposed", + "pair_status": "bulk_GSM_has_no_column_in_author_count_table" + }, + { + "sc_gsm": "GSM6249267", + "sample_id": "80A16A_d0", + "group": "exposed", + "pair_status": "bulk_GSM_has_no_column_in_author_count_table" + }, + { + "sc_gsm": "GSM6249268", + "sample_id": "80A16A_d14", + "group": "exposed", + "pair_status": "bulk_GSM_has_no_column_in_author_count_table" + }, + { + "sc_gsm": "GSM6249272", + "sample_id": "E0FA1E_dNA", + "group": "healthy", + "pair_status": "bulk_GSM_has_no_column_in_author_count_table" + }, + { + "sc_gsm": "GSM6249273", + "sample_id": "3F3322_dNA", + "group": "healthy", + "pair_status": "bulk_GSM_has_no_column_in_author_count_table" + }, + { + "sc_gsm": "GSM6249274", + "sample_id": "94D44E_dNA", + "group": "healthy", + "pair_status": "bulk_GSM_has_no_column_in_author_count_table" + }, + { + "sc_gsm": "GSM6249275", + "sample_id": "52BA23_dNA", + "group": "healthy", + "pair_status": "bulk_GSM_has_no_column_in_author_count_table" + }, + { + "sc_gsm": "GSM6249276", + "sample_id": "655A91_dNA", + "group": "healthy", + "pair_status": "bulk_GSM_has_no_column_in_author_count_table" + } + ], + "author_cohort_vs_geo_exposure": { + "0BF51C": { + "author_cohort": "Moderate", + "geo_exposure": "Severe" + }, + "0E1F8E": { + "author_cohort": "Moderate", + "geo_exposure": "Severe" + }, + "180E1A": { + "author_cohort": "Moderate", + "geo_exposure": "Severe" + }, + "3F05F3": { + "author_cohort": "Moderate", + "geo_exposure": "Severe" + }, + "40067F": { + "author_cohort": "Moderate", + "geo_exposure": "Severe" + }, + "82CCF5": { + "author_cohort": "Moderate", + "geo_exposure": "Severe" + }, + "B85D75": { + "author_cohort": "Moderate", + "geo_exposure": "Severe" + } + }, + "rule": "A pair is one sc GEX GSM and one bulk GSM with the same GEO subject ID and the same GEO sampling day (title ', , , ' = characteristics subject/time); both GSMs must agree on GEO age, sex, exposure group and serostatus; and the bulk GSM must have a column in the author featureCounts table (column '-' for infected/exposed subjects, '' for healthy). 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explicitly indexed captures combined per donor, QC-pass raw sum rescaled by 1000/total_QC_cells; expected-aggregate target, not an actual 1000-cell subsample", + "bulk_preprocessing": "Native STAR gene counts primary; SC-training-depth matched counts sensitivity; no length normalization primary", + "sensitivity_modes": ["bulk_depthmatched_to_native_expected_pseudo", "both_modalities_depthmatched"], + "conditioner": "Existing frozen E2 full-axis cache; exact full20097 transform followed by panel selection; gene and scalar features clipped as original; mean offset added without further clipping for condition-space evaluation only", + "sample_sizes": [2, 4, 6, 8, 12, 16, 24, 32, 48, 64, 80, 107], + "bootstrap_repeats": 1000, + "heldout_resamples": 200, + "seed": 20260914, + "primary_numerical_endpoint": "95th percentile of gene-offset RMS error, in original training-standardized units, under iid donor bootstrap with replacement against the empirical107 population mean", + 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below the all-other-pools reference in at least90 percent of conditional calibration resamples; report aggregate and each heldout pool", + "uncertainty": "Bootstrap and resample intervals describe conditional sampling sensitivity, not independent-cohort confidence intervals; seven pool results reported separately", + "pool_effect": "Exploratory unbalanced one-way random-effects method-of-moments variance decomposition on paired difference vectors; descriptive only, seven pools", + "restrictions": ["No GPU or generator inference", "No claim of universal minimum across protocols or disease cohorts", "No finite-population correction in iid bootstrap stability curve", "Raw acquisition and prior artifacts preserved", "No sample-specific SC metadata input in bulk K/depth conventions", "No multiple-testing significance claim; threshold curves and effect sizes are descriptive"] +} diff --git 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