Considerable effort in experimental quantum computing is devoted to noisy intermediate scale quantum computers (NISQ computers). Understanding the effect of noise is important for various aspects of this endeavor including notable claims for achieving quantum supremacy and attempts to demonstrate quantum error correcting codes. In this paper we use Fourier methods combined with statistical analysis to study the effect of noise. In particular, we use Fourier analysis to refine the linear cross-entropy fidelity estimator. We use both analytical methods and simulations to study the effect of readout and gate errors, and we use our analysis to study the samples of Google's 2019 quantum supremacy experiment.