Required condition to run the False Positive Rate algorithm:

• Selected User context must be grouped

If above condition is respected, then follow these steps:

1. Select the User context for which you want to compute the FPR
2. Right-click on the selected context and select Algorithms→Compute False Positive Rate
   • Or, from the main toolbar, select MS Identifications→Context→Algorithms→Compute False Positive Rate
3. A progress bar will appear on the screen
   
4. When process is finished, a dialog message will appear to display the FPR in percentage:
   
5. Result can also be retrieved in the Context properties:
   

The Formula used to compute False Positive Rate is:

• FPR = ∑FP/(∑TP+∑FP)
• with FP = (2*reverse). This FP value is get from the “significant.and.duplicated.fp” identification property.
• with TP = (reverse+forward) - FP. This TP value is get from the “significant.and.duplicated.tp” identification property.
• ∑FP represents the sum of all “significant.and.duplicated.fp” values (i.e. the sum of the “significant.and.duplicated.fp” property of all identifications under the context)
• ∑TP represents the sum of all “significant.and.duplicated.tp” values (i.e. the sum of the “significant.and.duplicated.tp” property of all identifications under the context)

The user can retrieve the significant.and.duplicated.fp and significant.and.duplicated.tp of all the identifications in the log.

If one (or more) identification contains a zero value for one or both properties,
this identification is not taken into account in the calculation.

For example, in the screen shot on the left, you can read that 895 out of 959 identifications were used for the calculation.

The user is informed about this in the resulting dialog message and in the context properties:

You can see computed False Positive Rate in the Context properties:

- Select the User context for which FPR has already been computed - Right-click on the selected context and select Properties - The False Positive Rate appears under the “false positive” category:

• significant.and.duplicated.rate is the rate in percentage.