A case-control study design may potentially over-estimate the predictive value of a test, but we have attempted to eliminate further bias by comparing the tests using an independent reference standard (microbiologically confirmed disease) according to STARD guidelines.
Mass accuracy and reproducibility were maintained by using an independent reference spray (LockSpray; Waters).
Data were centroided during acquisition using an independent reference lock-mass ion via the LockSpray™ interface to ensure accuracy and precision.
For the time course study, TCDD-treated samples were compared to time-matched vehicle controls using an independent reference design [ 49].
Temporal changes in gene expression were assessed using an independent reference design in which samples from EE and TAM treated animals were co-hybridized with VEH.
Temporal changes in gene expression were assessed using an independent reference design in which o, p'-DDT-treated samples were co-hybridized with time-matched vehicle controls using 3 biological replicates and 2 independent labelings of each sample (i.e. dye swap) for each time point.
These results are only slightly lower than the accuracy rate calculated for SIRENE on the normal ovarian data (as assessed using an independent reference network), and slightly higher than expected based on the performance of SIRENE on the synthetic DREAM datasets.
Moreover, some spoligotype signatures could also be used as an independent reference for congruence analysis, especially when LSP analysis was not informative.
However, the present study evaluates whether already existing protocols may be used as an independent reference standard to evaluate the appropriateness of triage recommendations in a pilot design.
We have not used Release 6 because it incorporated the data from Krsticevic et al. (2010) (Hoskins et al. 2015) and hence cannot be used as an independent reference.
