In this paper, the Generalized Cell Mapping (GCM) method for a linear system is compared with a new stochastic method for novel cell-to-cell mapping. The authors presented the new stochastic method in Mohon and Pisu (2013). The two methods are compared in an application example of a vehicle alternator. The alternator may experience three faults including belt slippage, a faulty diode connection, or incorrect controller reference voltage. Fault detection and isolation (FDI) is performed using the two cell-to-cell mapping methods. The results show that the new stochastic method is slower but yields better isolation results than the GCM method.