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In order to meet common fuel specifications such as cetane number and volatility, a refinery must blend a number of refinery stocks derived from various process units in the refinery. Fuel chemistry can be significantly altered in meeting fuel specifications. Additionally, fuel specifications are seldom changed in isolation, and the drive to meet one specification may alter other specifications. Homogeneous charge compression ignition (HCCI) engines depend on the kinetic behavior of a fuel to achieve reliable ignition and are expected to be more dependent on fuel specifications and chemistry than today's conventional engines. Regression analysis can help in determining the underlying relationships between fuel specifications, chemistry, and engine performance. Principal Component Analysis (PCA) is used as an adjunct to regression analysis in this work, because of its ability to deal with co-linear variables and potential to uncover ‘hidden’ relationships between the variables.