In this paper we present the methodology developed to analyze the detector response of neutron noise experiments performed at EPFL CROCUS and TUD AKR-2 reactors in the framework of the H2020 CORTEX project. The noise, or modulation, is induced by controlled oscillations of neutron absorbers or reactor fuel elements. The quantities of interest are detector response spectral power and phase shift with respect to a selected reference detector. For the analysis we employ data normalization and bootstrapping with replacement. It acts as a frequency response comb, letting through only the harmonics of the base oscillation frequency, and eliminates biases due to correlations of consecutive oscillations while maintaining the frequency resolution of the original data set. The correlations stemming from a common neutron noise inducing device are also considered in the analysis.