An increasing demand for an extended flexibility to model types and production volumes in the manufacture of large-size assemblies has generated a growing interest in the reduction of jigs and fixtures deployment during assembly operations. A key factor enabling and sustaining this reduction is the constantly expanding availability of instruments for dimensional measurement of large-size products. However, the increasing complexity of these measurement systems and their set-up procedures may hinder the final users in their effort to assess whether the performance of these instruments is adequate for pre-specified inspection tasks. In this paper, mixed-effects and fixed-effects linear statistical models are proposed as a tool to assess quantitatively the effect of set-up procedures on the uncertainty of measurement results. This approach is demonstrated on a Metris Indoor GPS system (iGPS). The main conclusion is that more than 99% of the variability in the considered measurements is accounted for by the number of points used in the bundle adjustment procedure during the set-up phase. Also, different regions of the workspace have significantly different error standard deviations and a significant effect on the transient duration of measurement. This is expected to affect adversely the precision and unbiasedness of measurements taken with Indoor GPS when tracking moving objects.