  We use Principal Component Analysis (PCA) to study the gas dynamics in
numerical simulations of typical MCs. Our simulations account for the
non-isothermal nature of the gas and include a simplified treatment of the
time-dependent gas chemistry. We model the CO line emission in a
post-processing step using a 3D radiative transfer code. We consider mean
number densities n_0 = 30, 100, 300 cm^{-3} that span the range of values
typical for MCs in the solar neighbourhood and investigate the slope
\alpha_{PCA} of the pseudo structure function computed by PCA for several
components: the total density, H2 density, 12CO density, 12CO J = 1 -> 0
intensity and 13CO J = 1 -> 0 intensity. We estimate power-law indices
\alpha_{PCA} for different chemical species that range from 0.5 to 0.9, in good
agreement with observations, and demonstrate that optical depth effects can
influence the PCA. We show that when the PCA succeeds, the combination of
chemical inhomogeneity and radiative transfer effects can influence the
observed PCA slopes by as much as ~ +/- 0.1. The method can fail if the CO
distribution is very intermittent, e.g. in low-density clouds where CO is
confined to small fragments.
