A silicon-based fine granularity calorimeter is a potential technology for the future International Linear Collider ILC, the future circular collider CEPC, and is also the chosen technology for the upgraded CMS experiment of the Large Hadron Collider. Active silicon sensing pads are used as MIP counters and the standard calibration of the calorimeter uses weights based on the average energy loss, $dEdx$. In this work, the limitations of the dEdx calibration method in terms of energy linearity, scale and resolution are explored. In the case of a calorimeter with varying passive layer thickness as the one planned for CMS, the $dEdx$ method leads to a significant constant term in the resolution function and a non-linearity of energy response. For these reasons, a method based on the calorimeter sampling fraction that exploits the per-event measured shower depth is presented and shown to deliver superior absolute energy scale, linearity and resolution. Calorimetric designs in which the back of the shower is sampled less, offer reduced cost without loss in performance. Therefore, a proper calibration as proposed here is crucial in obtaining the most cost- and performance-effective silicon-sampling calorimeter design.