In many fields of the natural sciences, from biology to physics, advanced data analysis tools are acquiring more and more importance to investigate difficult problems. A typical application is synchronization experiments, which involve coupled quantities, a “target” and a “driver”, with quasi-periodic behaviours. Unfortunately, in complex systems very rarely a couple of quantities can be really considered fully isolated and immune from other influences. It is therefore important to consider not only the legacy of their past, but also the possible effects of additional confounding factors. In order to tackle this problem, an advanced application of the recurrence plots, called Conditional Recurrence plots, has been developed. The potential of the innovative technique has been confirmed by comparison with the conditional transfer entropy, the traditional technique used to address these problems. Preliminary results from experimental data of sawteeth pacing with radio frequency modulation are very encouraging. Being quasi-periodic, sawteeth occurs naturally and, especially in H mode plasmas, the effectiveness of the pacing with radiofrequency heating can be difficult to establish. The proposed data analysis procedure is aimed at better discounting the confounding factors, like natural sawteeth, providing both a more accurate quantification of the pacing efficiency and a deeper insight into the physical processes involved, thanks to a better understanding of the relevant causal relations.