A photonic crystal waveguide (PhC-WG) was reported to be usable as an optical sensor highly sensitive to various material parameters, which can be detected via changes in transmission through the PhC-WG caused by small changes of the refractive index of the medium filling its holes. To monitor these changes accurately, a precise optical model is required, for which the plane wave expansion (PWE) method is convenient. We here demonstrate the revision of the PWE method by employing the complex Fourier factorization approach, which enables the calculation of dispersion diagrams with fast convergence, i.e., with high precision in relatively short time. The PhC-WG is proposed as a line defect in a hexagonal array of cylindrical holes periodically arranged in bulk silicon, filled with a variable medium. The method of monitoring the refractive index changes is based on observing cutoff wavelengths in the PhC-WG dispersion diagrams. The PWE results are also compared with finite-difference time-domain calculations of transmittance carried out on a PhC-WG with finite dimensions.