depinwang/jinyang-gse138866-splicing-subtypes-results-v1
jinyang-gse138866-splicing-subtypes-results-v1 Canary run (N=110 real GSE138866 samples) for AS-based consensus-clustering molecular subtype discovery. Outcome: GATE_FAILURE (null result). Only 2/10,019 high-confidence AS events clear BH-FDR<0.05 (need >=20 to proceed to clustering) -- a pre-specified valid stopping point ("insufficient power to detect stable AS-based subtypes"), not a pipeline bug. Downstream clustering/KM/permutation-null artifacts were not produced, per… See the full description on the dataset page: https://huggingface.co/datasets/depinwang/jinyang-gse138866-splicing-subtypes-results-v1.
jinyang-gse138866-splicing-subtypes-results-v1
Canary run (N=110 real GSE138866 samples) for AS-based consensus-clustering molecular subtype discovery. Outcome: GATE_FAILURE (null result). Only 2/10,019 high-confidence AS events clear BH-FDR<0.05 (need >=20 to proceed to clustering) -- a pre-specified valid stopping point ("insufficient power to detect stable AS-based subtypes"), not a pipeline bug. Downstream clustering/KM/permutation-null artifacts were not produced, per design.
A central-validity check (independent of the clustering question) found that RNA-quality covariates (TIN, PSI-missingness) directly predict overall survival in this cohort (tinmedian p=0.0007, psimissingness_full p=0.0008) -- FFPE/RNA-quality is itself prognostic here, which is a real confound risk for any future AS-based subtyping attempt on this cohort.
See notes/experiments/jinyang-gse138866-splicing-subtypes/ in the RACA workspace for the full pre-registered design (experiment.yaml), 8 rounds of red-team review (red_team_brief.md), and this run's activity log.
Configs
from datasets import load_dataset
cox = load_dataset("depinwang/jinyang-gse138866-splicing-subtypes-results-v1", "candidate_events_cox", split="train")