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Fundamentals of experimental design for cDNA microarrays

Nature Genetics volume 32, pages 490–495 (2002)Cite this article

Abstract

Microarray technology is now widely available and is being applied to address increasingly complex scientific questions. Consequently, there is a greater demand for statistical assessment of the conclusions drawn from microarray experiments. This review discusses fundamental issues of how to design an experiment to ensure that the resulting data are amenable to statistical analysis. The discussion focuses on two-color spotted cDNA microarrays, but many of the same issues apply to single-color gene-expression assays as well.

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Figure 1: A schematic representation of the three layers of design in a simple microarray experiment.

Bob Crimi

Figure 2: Experimental designs for the direct comparison of two samples.
Figure 3: Experimental designs using a reference RNA sample.
Figure 4: Common features in the layout of a microarray slide.
Figure 5: Two examples of one-way classifications with replication.
Figure 6: Experimental design for a 3 × 2 factorial experiment.

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Acknowledgements

Support for this work was provided by the US National Institutes of Health. The analogy of measuring one man and one woman is attributed to Peter Petraitis.

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  1. The Jackson Laboratory, 600 Main Street, Bar Harbor, 04609, ME, USA

    Gary A. Churchill

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  1. Gary A. Churchill
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Churchill, G. Fundamentals of experimental design for cDNA microarrays. Nat Genet 32 (Suppl 4), 490–495 (2002). https://doi.org/10.1038/ng1031

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