One goal of the IERS to define and maintain the ITRF is to combine all major space geodetic techniques (GPS, VLBI, SLR, LLR and DORIS solution in the SINEX format) into an integrated consistent set of high-accuracy products. In such a combination, estimating and removing the systematic errors between different SINEX files is an important issue. For this purpose software GNAS (Geodesy Network Analysis System) is developed, which is able to estimate 7 Helmert transformation parameters of station coordinates within the process of combination. Besides, the GNAS software enables us to combine EOPs and station coordinates not only separately, but also simultaneously. We discuss the advantages and disadvantages when systematic parameters are estimated for each Analysis Center (AC) or for each SINEX file. One can estimate either the whole 7 Helmert parameters or only a set of them (e.g. without 3 rotation parameters). Different procedures have different effects on the combined solutions, especially when EOPs and station coordinates are combined simultaneously. Detailed discussions, numerical examples and some results analysis are given in this paper.