Design of Large Time-Course Microarray Experiments with Two Channels

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In this article we propose two practical types of designs for large time-course, dual-channel microarray experiments. One type consists of several interwoven loops, and the other type combines reference and loop designs. By representing the experiment as a graph, where the timepoints are nodes and the arrays are edges, we demonstrate how the time contrasts between any two timepoints can be estimated, provided that there is a path of edges linking them. In addition, we give a general formula for the variance of such contrasts. The efficiency of the proposed designs is evaluated by estimating the variances of the log-ratios of the comparisons of interest.

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The authors are grateful to Agostino Nobile (University of Glasgow) for the suggestion to consider a carriage wheel design, for interesting discussions on the subject of design of microarray experiments and for valuable comments on this paper.

This research has been funded by the Biotechnology and Biological Sciences Research Council (BBSRC), UK, programme ‘Exploiting Genomics’.

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Correspondence to Dr Raya Khanin.

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Khanin, R., Wit, E. Design of Large Time-Course Microarray Experiments with Two Channels. Appl-Bioinformatics 4, 253–261 (2005).

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  • Outer Loop
  • Distant Point
  • Efficient Design
  • Loop Design
  • Consecutive Point