Chapter 9. Microarray Gene Expression: The Effects of Varying Certain Measurement Conditions

  1. Andreas Scherer Founder/CEO of Spheromics
  1. Walter Liggett1,
  2. Jean Lozach2,
  3. Anne Bergstrom Lucas3,
  4. Ron L Peterson4,
  5. Marc L Salit5,
  6. Danielle Thierry-Mieg6,
  7. Jean Thierry-Mieg6 and
  8. Russell D Wolfinger7

Published Online: 2 NOV 2009

DOI: 10.1002/9780470685983.ch9

Batch Effects and Noise in Microarray Experiments: Sources and Solutions

Batch Effects and Noise in Microarray Experiments: Sources and Solutions

How to Cite

Liggett, W., Lozach, J., Lucas, A. B., Peterson, R. L., Salit, M. L., Thierry-Mieg, D., Thierry-Mieg, J. and Wolfinger, R. D. (2009) Microarray Gene Expression: The Effects of Varying Certain Measurement Conditions, in Batch Effects and Noise in Microarray Experiments: Sources and Solutions (ed A. Scherer), John Wiley & Sons, Ltd, Chichester, UK. doi: 10.1002/9780470685983.ch9

Editor Information

  1. Spheromics, Kontiolahti, Finland

Author Information

  1. 1

    Statistical Engineering Division, National Institute of Standards and Technology, Gaithersburg, MD, USA

  2. 2

    Illumina Inc., San Diego, CA, USA

  3. 3

    Genomics R&D, Life Sciences Solution Unit, Agilent Technologies Inc., Santa Clara, CA, USA

  4. 4

    Biopharma Consultant, North Chelmsford, MA, USA

  5. 5

    Multiplexed Biomolecular Science Group, National Institute for Standards and Technology, Gaithersburg, MD, USA

  6. 6

    AceView Integrative Gene Annotation Group, National Institute of Health, Bethesda, MD, USA

  7. 7

    SAS Institute Inc., Cary, NC, USA

Publication History

  1. Published Online: 2 NOV 2009
  2. Published Print: 30 OCT 2009

ISBN Information

Print ISBN: 9780470741382

Online ISBN: 9780470685983

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Keywords:

  • Agilent platform;
  • animal study;
  • biological variation;
  • control group;
  • gauge repeatability and reproducibility;
  • high dimension;
  • linear mixed model;
  • measurement assurance;
  • measurement protocol;
  • titration mixture

Summary

This chapter explores measurements from an experiment with a batch effect induced by switching the mass of RNA analyzed from 400 ng to 200 ng. The experiment has as additional factors the RNA material (liver, kidney, and two mixtures) and the RNA source (six different animals). We show that normalization can partially correct the batch effect. On the basis of the normalized intensities, we compare, gene by gene, the size of the batch effect with the animal-to-animal variation. These comparisons show that the animal variation is larger or smaller depending on which gene is considered. We present gene-by-gene tests of the linearity of the microarray response. In addition, we present data analysis results that suggest other batch effects.