A common approach in fault diagnosis is monitoring the deviations of measured variables from the values at normal operations to identify the root causes of faults. When the number of conceivable faults is larger than that of predictive variables, conventional approaches can yield ambiguous diagnosis results including multiple fault candidates. To address the issue, this work proposes a fault magnitude based strategy. Signed digraph is first used to identify qualitative relationships between process variables and faults. Empirical models for predicting process variables under assumed faults are then constructed with support vector regression (SVR). Fault magnitude data are projected onto principal components subspace, and the mapping from scores to fault magnitudes is learned via SVR. This model can estimate fault magnitudes and discriminate a true fault among multiple candidates when different fault magnitudes yield distinguishable responses in the monitored variables. The efficacy of the proposed approach is illustrated on an actuator benchmark problem.