PaGE 5.0 Documentation - the "direct comparison design"

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

In the direct comparison design 2-channel arrays are used, with condition 0 being hybridized to one channel and condition 1 hybridized to the other. Since we do not separate the channels, but instead work directly with the ratios, this requires an analysis which is somewhat different from the 1-channel or reference design.
 
See also Reference Design and Study Design