Hybridization spots have to be identified and further analyzed. However, shape and size of the spots fluctuate significantly across the array. These fluctuations are caused by printing, hybridization, and slide-surface chemistry factors, which can significantly affect the interpretation of the microarray image. Spot position variation is caused by inherent mechanical limitations of the spotting process, for example, vibration of the printing pins within the pinhead and vibrations of the platform. Microarray images consist of arrays of spots arranged in grids.
All grids have the same numbers of rows and columns of spots.
Typically, each pin of the robotic arrayer deposits DNA material in a single subgrid. Each array element is called a pixel, or picture element, and is represented in the computer as an integer value. A higher sensitivity allows for finer differentiation in the range of intensity values. A 16-bit representation produces up to 65,536 different shades of gray. Precise identification of signal pixels for microarray spots is crucial for obtaining accurate data in expression analysis.