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Recommendation To Use Exact P-Values In Biomarker Discovery Research, Margaret Sullivan Pepe, Matthew F. Buas, Christopher I. Li, Garnet L. Anderson
Recommendation To Use Exact P-Values In Biomarker Discovery Research, Margaret Sullivan Pepe, Matthew F. Buas, Christopher I. Li, Garnet L. Anderson
UW Biostatistics Working Paper Series
Background: In biomarker discovery studies, markers are ranked for validation using P-values. Standard P-value calculations use normal approximations that may not be valid for small P-values and small sample sizes common in discovery research.
Methods: We compared exact P-values, valid by definition, with normal and logit-normal approximations in a simulated study of 40 cases and 160 controls. The key measure of biomarker performance was sensitivity at 90% specificity. Data for 3000 uninformative markers and 30 true markers were generated randomly, with 10 replications of the simulation. We also analyzed real data on 2371 antibody array markers …