A detectability floor for treatment-response labels in rheumatology transcriptomics

Objectives. Before-and-after transcriptomics in rheumatic disease often yields no reproducible treatment signal, though disease-state stratification is robust. We asked whether exposure and response-prediction labels fall below the detection floor of the designs defining them, while matched disease-state labels do not. Methods. Eight public datasets were analysed (paired juvenile dermatomyositis n = 10; RA before/after methotrexate, n = 28 pairs; lupus nephritis n = 10; controlled exposures; a single-cell dose series). Response labels in current use (one benchmark trajectory, five published si

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