Novel comparison of evaluation metrics for gene ontology classifiers reveals drastic performance differences
Fig 2
In this toy example we start with a set of correct annotations using only two GO terms A and B, taken from truth set T. Initially, in the upper part the Artificial Prediction Set (APS) matches perfectly to T. This would give us 100% correct predictions. Next, the permutation step, shown in the middle, switches GO terms for a pair of genes. This increases false positives and false negatives by 1 and decreases true positives and true negatives by 1. We obtain as a result an APS with a known level of errors (0.002 in this example). The permutation is repeated with other gene pairs and other GO terms until the required noise level is obtained.