Resolution:
## Figure 2.
Average cumulative number of false positives versus . Average cumulative number of false positives versus E-valuesE-values. Theoretically speaking, average number of false positives with E-values less than or equal to a cutoff E_{c }should be E_{c }provided that the number of trials is large enough. The accuracy of E-values assigned by RAId_DbS is tested along with three other methods, X! Tandem(v1.0),
Mascot(v2.1) and OMSSA(v2.0). For X! Tandem, Mascot and OMSSA searches, default parameters
of each program are used except the maximum number of miscleavages, which is set to
3 uniformly for this test. The diagonal solid lines in each panel are the theoretical
lines. There are two curves associated with each method. The dashed line corresponds
to the results using regular nr. The solid line corresponds to the results using nr
with cluster removal, which we anticipate to be a better representative of a random
database. See text for additional details.
Alves |