It is hard if not impossible , without knowing the underlying truth , to get good estimates of detection sensitivity and specificity or other direct accuracy measures , so we evaluated the rankings of potential pairs by related validation data for comparison and assessment of different methods . Using related Hi - C data , we created Aggregate Peak Analysis ( APA ) plots and found that the ranking of potential pairs by ChIAPoP is better than those by other methods . We used FDR - adjusted P - values to rank the pairs for each method , except for ChiaSig which only outputs P - values .   In a parenthesis is the proportion of the corresponding significant pairs in all significant pairs detected by the more conservative method ( either ChiaSig or mango ) .