1. A method for evaluating an orientation of a molecular array having features arranged in a pattern, comprising: (a) receiving an image of the molecular array produced by scanning the molecular array to determine data signals emanating from discrete positions on a surface of the molecular array; (b) calculating an actual result of a function on pixels of the image along an axis of the image; (c) comparing the result of step (b) with an expected result that would be obtained if the features were arranged in a pattern having a predetermined orientation.