Figure 2. False positives (FP) performance of RATs as a function of replication level.

False positive fraction measured over 100 permutation iterations of randomly selected (without replacement) replicates from a pool of 16 high-quality wild-type Colombia-0 Arabidopsis thaliana replicates from Froussios et al. (2017, ²⁹). [ A] FP fraction of each bootstrap iteration, for default values of all RATs parameters (v0.6.2), across a range of replication levels, separately for the gene-level test (red) and transcript level test (blue). [ B] Mean FP fraction by replication level, as a function of the effect size threshold (effect size = difference between conditions of an isoform’s proportion). For a gene, the effect size is defined as the largest proportion difference observed among that gene’s isoforms. In every iteration, the FP fraction was calculated against the number of genes or transcripts that were eligible for testing each time (a number which remains very stable across iterations and replication levels – see Extended data 1 ³³).