In this letter, we compare three polynomial chaos expansion (PCE)-based methods for ANCOVA (ANalysis of COVAriance) indices based global sensitivity analysis for correlated random inputs in two power system applications. Surprisingly, the PCE-based models built with independent inputs after decorrelation may not give the most accurate ANCOVA indices, though this approach seems to be the most correct one and was applied in [1] in the field of civil engineering. In contrast, the PCE model built using correlated random inputs directly yields the most accurate ANCOVA indices for global sensitivity analysis. Analysis and discussions about the errors of different PCE-based models will also be presented. These results provide important guidance for uncertainty management and control in power system operation and security assessment.