Timing techniques offer powerful tools to study dynamical astrophysical phenomena. In the X-ray band, they offer the potential of probing accretion physics down to the event horizon. Recent work has used frequency and energy-dependent time lags as a tool for studying relativistic reverberation around the black holes in several Seyfert galaxies. This was achieved thanks to the evenly-sampled light curves obtained using XMM-Newton. Continuous-sampled data is however not always available and standard Fourier techniques are not applicable. Here, building on the work of Miller et al. (2010), we discuss and use a maximum likelihood method to obtain frequency-dependent lags that takes into account light curve gaps. Instead of calculating the lag directly, the method estimates the most likely lag values at a particular frequency given two observed light curves. We use Monte Carlo simulations to assess the method's applicability, and use it to obtain lag-energy spectra from Suzaku data for two objects, NGC 4151 and MCG-5-23-16, that had previously shown signatures of iron K reverberation. The lags obtained are consistent with those calculated using standard methods using XMM-Newton data.