A multivariate statistical approach is presented to analyze the changes in calculated harmonic vibrational frequencies and infrared intensities obtained from ab initio calculations for methane and silane. The effects of four wave function modifications on these spectral parameters are investigated using a two-level factorial design and principal component analyses: basis set (6-31G and 6-311G), inclusion of polarization and diffuse functions as well as electron correlation treatment using the second-order Møller-Plesset method. Characteristic group frequencies present similar factorial models for each molecule. However, the intensity factorial models are quite different for these group vibrations. The most important effect values for the methane frequencies are due to a change from the Hartree-Fock to the second-order Møller-Plesset level. However, this effect is secondary to the one provoked by the inclusion of polarization functions in the silane basis set.