In this paper we demonstrate that the structural and optical properties of Si nanoclusters (Si ncs) formed by thermal annealing of SiOx films prepared by plasma enhanced chemical vapor deposition (PECVD) and magnetron sputtering are very different. In fact, at a fixed Si excess and annealing temperature, photoluminescence (PL) spectra of sputtered samples are redshifted with respect to PECVD samples, denoting a larger Si ncs size. In addition, PL intensity reaches a maximum in sputtered films at annealing temperatures much lower than those needed in PECVD films. These data are correlated with structural properties obtained by energy filtered transmission electron microscopy and electron energy loss spectroscopy. It is shown that in PECVD films only around 30% of the Si excess agglomerates in clusters while an almost complete agglomeration occurs in sputtered films. These data are explained on the basis of the different initial structural properties of the as-deposited films that become crucial for the subsequent evolution.