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Extending the loop design for two-channel microarray experiments

Published online by Cambridge University Press:  19 March 2007

NAOMI S. ALTMAN  and
JUN HUA
NAOMI S. ALTMAN
Affiliation:
Department of Statistics, Thomas Building, The Pennsylvania State University, University Park, PA 16801-2111, USA
JUN HUA
Affiliation:
Department of Statistics, Thomas Building, The Pennsylvania State University, University Park, PA 16801-2111, USA
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Abstract

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The loop design of Kerr and Churchill is a clever application of incomplete blocks of size 2 to two-channel microarray experiments. In this paper, we extend the loop design to include more replicates, biological and technical replication, multi-factor experiments, and blocking. Loop and extended loop designs are shown to be more efficient than the reference design for any given number of arrays. We also show that adding new treatments to a loop design requires the same number of additional arrays as adding treatments to a reference design, with a greater gain in power. Given the flexibility of extended loop designs and their power, we propose that these should be the designs of choice for most experiments using two-channel microarrays.

Type
Research Article
Information
Genetics Research , Volume 88 , Issue 3 , December 2006 , pp. 153 - 163
Copyright
2006 Cambridge University Press