1. A method comprising the steps of: (a) providing a laser source, a detector and scanner optics, said laser source being constructed and arranged to produce excitation radiation being delivered to an array including hybridized probe-target pairs, said detector being constructed to detect emitted radiation excited in a fluorophore in response to the excitation radiation, and said scanner being constructed to scan the probe array to generate image data based on sampled emission radiation received from said detector over a pixel array corresponding to the scanned probe array; (b) providing in a graphical user interface (GUI) at least the following windows: (i) a first window having a plurality of image features based on the image data, each having one or more characteristics representing one or more hybridization reactions associated with a probe of a probe array, (ii) a second window having a plurality of data features, each relating to one or more quantifications of one or more hybridization reactions associated with a probe of the probe array, and (iii) a third window having a plurality of descriptive features, each feature including at least two descriptive elements selected from the group consisting of: absolute image intensity value, probe data links, pin identifier, well plate identifier, chromosome location of a gene represented by the probe, chromosome location of an expressed sequence tag represented by the probe, band location on the chromosome, a single-nucleotide polymorphism (SNP) identifying the location on the chromosome, a non-SNP marker identifying the location on the chromosome, data related to the production of hybridization intensity data displayed in the first window, and information about the targets that hybridized with the probes.