Microarray Databases: Storage and Retrieval of Microarray Data

Microarray experiments rely on and generate (1 –3 ) quantities of data that are simply too large to be stored on a researcher’s desktop computer in spreadsheet format. A single microarray may have 40,000 spots. Associated with each spot may be as many as 40 different metrics, and an experimental series may consist of many dozens of such microarrays. Thus, to manage microarray data effectively, a microarray database is required; indeed, a database is not a luxury when carrying out microarray experiments—it is a necessity. In this chapter, we examine some of the properties that a microarray database should have. While this chapter focuses on the needs for tracking and storing data associated with spotted glass microarrays in particular, most of the considerations are pertinent to storage of large-scale expression data obtained on other platforms, such as Affymetrix gene chips, and nylon arrays.