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