We examine both experimental and simulated data of the optical transmission response of nanohole arrays in metal films to bulk and surface refractive index changes. We compare the signal-to-noise performance of the following three different analysis methods: the conventional peak shift method, a normalized-difference integrated-response method that is commonly used in 3-D plasmonic crystals, and an integrated response (IR) method. Our IR method shows a 40% and 90% improvement in the signal-to-noise ratio (SNR) for bulk and surface binding tests, respectively, compared with the direct measurement of the transmission-peak wavelength shift, promising improved sensing performance for future nanohole-array sensor applications.