Patterns of neural data obtained from electroencephalography (EEG) can be classified by machine learning techniques to increase human-system performance. In controlled laboratory settings this classification approach works well; however, transitioning these approaches into more dynamic, unconstrained environments will present several significant challenges. One such challenge is an increase in temporal variability in measured behavioral and neural responses, which often results in suboptimal classification performance. Previously, we reported a novel classification method designed to account for temporal variability in the neural response in order to improve classification performance by using sliding windows in hierarchical discriminant component analysis (HDCA), and demonstrated a decrease in classification error by over 50% when compared to the standard HDCA method (Marathe et al., 2013). Here, we expand upon this approach and show that embedded within this new method is a novel signal transformation that, when applied to EEG signals, significantly improves the signal-to-noise ratio and thereby enables more accurate single-trial analysis. The results presented here have significant implications for both brain-computer interaction technologies and basic science research into neural processes.