How does MetaboAnalyst calculate 95% confidence intervals (CIs) of AUC/pAUC (biomarker analysis)?

The program uses a non-parametric re-sampling based approach for calculating the confidence intervals. In either bootstrap (classical) or MCCV (multivariate) approach, the data are re-sampled many times, with the AUC/pAUC calculated each time.

Confidence intervals are then estimated by simply sorting the data and taking the percentiles to our desired confidence interval bounds. For instance, in 1000 resampling, 95% CIs will be the 25th and 975th values of the sorted AUC values. For details, please refer to the paper by T.A. Lasko et al..