* An array or slide is a collection of features spatially arranged in a two dimensional grid, arranged in columns and rows.
* Block or subarray: a group of spots, typically made in one print round; several subarrays/ blocks form an array.
* Case/control: an experimental design paradigm especially suited to the two-colour array system, in which a condition chosen as control (such as healthy tissue or state) is compared to an altered condition (such as a diseased tissue or state).
* Channel: the fluorescence output recorded in the scanner for an individual fluorophore and can even be ultraviolet.
* Dye flip or dye swap or fluor reversal: reciprocal labelling of DNA targets with the two dyes to account for dye bias in experiments.
* Scanner: an instrument used to detect and quantify the intensity of fluorescence of spots on a microarray slide, by selectively exciting fluorophores with a laser and measuring the fluorescence with a filter (optics) photomultiplier system.
* Spot or feature: a small area on an array slide that contains picomoles of specific DNA samples.
* For other relevant terms see:
** Glossary of gene expression terms
** Protocol (natural sciences)