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Use of external controls in microarray experiments.

Ivana V Yang1

  • 1Laboratory of Respiratory Biology, National Institute of Environmental Health Sciences, National Institute of Health, Research Triangle Park, NC, USA.

Methods in Enzymology
|August 31, 2006
PubMed
Summary
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External RNA controls help standardize DNA microarray analysis for gene expression. These spike-in controls improve data comparability across different methods and platforms, ensuring reliable genomic-scale results.

Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • DNA microarray analysis is a key genomic technique for studying gene expression.
  • This complex method involves multiple steps and varied protocols across labs.
  • Standardization is crucial for comparing data from different platforms.

Purpose of the Study:

  • To define external RNA controls and available spike-in control collections.
  • To explain the implementation of these controls in laboratory settings.
  • To discuss the applications of external controls in microarray analysis.

Main Methods:

  • Review of external RNA control concepts and types.
  • Description of available spike-in RNA control sets.
  • Explanation of laboratory implementation procedures.

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Main Results:

  • External controls enable assessment of gene expression measurement variability.
  • Spike-in controls facilitate data comparison across diverse microarray platforms and protocols.
  • Applications include performance assessment, normalization, algorithm evaluation, and mRNA quantification.

Conclusions:

  • External RNA controls are essential for robust and comparable DNA microarray gene expression studies.
  • Their use enhances the reliability of genomic-scale data analysis.
  • Standardization through controls supports advanced applications like absolute mRNA quantification.