It is of interest to compare and combine immune responses from two independent samples measured by the same type of assay across different laboratories. Inter-laboratory variations will need to be adjusted for in this process to achieve valid inferences. We address this problem for continuous assay via integration of external data, collected on paired samples from the same two laboratories. We consider approaches for estimation and testing of the mean difference of the two independent samples. Simulation results under a variety of scenarios demonstrate satisfactory finite sample performance of our proposed method. These results also provide guidance on the sample size requirement of paired-sample studies in order to obtain adequate power in such data integration across laboratories. We apply our methods to analyze real ELISPot assay data generated by two major HIV network laboratories.