PaGE 5.0 Documentation - the "direct comparison design"

The study design is set when you choose File New Analysis Type

The reference design, uses 2-channel data, where the experimental conditions are hybridized in one channel and a common reference is hybridized to the other channel. This common reference is identical for all arrays. In this case the data consist of ratios (or log ratios), where the denominator is always the gene's intensity in the reference sample, and the numerator is one or the other experimental condition. We refer to this design as a 2-sample design, because it produces two sets of intensities for each array element, corresponding to the two conditions.
 
See also Direct Comparison Design and Study Design