This thesis consists of two parts. The first part is on fractional factorial design, and the second part is on computer experiment. The first part has two chapters. In the first chapter, we use the concept of conditional main effect, and propose the CME analysis to solve the problem of effect aliasing in two-level fractional factorial design. In the second chapter, we study the conversion rates of a system of webpages with the proposed funnel testing method, by using directed graph to represent the system, fractional factorial design to conduct the experiment, and a method to optimize the total conversion rate with respect to all the webpages in the system. The second part also has two chapters. In the third chapter, we use regression models to quantify the model form uncertainties in the Perez model in building energy simulations. In the last chapter, we propose a new Gaussian process that can jointly model both point and integral responses.