 Solution

Define the evaluation universe first, including which sufficiently covered loci were eligible for both methods. Relative to the reference assay's labels,The true positive rate is the fraction of reference-positive loci retained by xPore; the false positive rate is the fraction of reference-negative loci incorrectly retained. The latter is not the fraction of xPore calls that fail validation.

An imperfect reference assay can miss real modifications. “False positive” here therefore means disagreement with that reference, not independently demonstrated absence of a modification. Restricting the universe differently for the two denominators would invalidate the comparison.