Standard Article

The use of external controls in microarray experiments

Part 2. Genomics

2.8. Expression Profiling

Basic Techniques and Approaches

  1. Joop M.L.M. van Helvoort,
  2. Dik van Leenen,
  3. Frank C.P. Holstege

Published Online: 15 OCT 2004

DOI: 10.1002/047001153X.g208407

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

How to Cite

van Helvoort, J. M., van Leenen, D. and Holstege, F. C. 2004. The use of external controls in microarray experiments. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. 2:2.8:102.

Author Information

  1. University Medical Center Utrecht, Utrecht, The Netherlands

Publication History

  1. Published Online: 15 OCT 2004

Abstract

Accuracy in reporting expression levels or differences therein is an important issue for microarray technology. Here we discuss the reasons for using external RNA controls for the optimization of nearly every aspect of microarray technology. The main conclusion is that external RNA controls offer an extremely versatile system that does not suffer from the disadvantages of other approaches and also lend themselves for assessing accuracy within every subsequent microarray experiment after optimization. We describe what external controls are, how they can contribute toward systematic analysis of accuracy, and how such controls should be implemented. Other uses of external controls such as normalization, determining sensitivity, and reporting absolute mRNA copies per cell are also discussed.

Keywords:

  • external controls;
  • spike-in controls;
  • accuracy;
  • variation;
  • normalization;
  • quantification;
  • mRNA copy per cell;
  • expression profiling;
  • microarray