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Bioinformatics Vol. 18 no. 12 2002
Pages 1609-1616
© 2002 Oxford University Press

Calculation of the minimum number of replicate spots required for detection of significant gene expression fold change in microarray experiments

Michael A. Black 1,3 and R. W. Doerge 1,2,3,*

1 Department of Statistics, Purdue University, West Lafayette, IN 47907, USA
2 Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA
3 Computational Genomics, Purdue University, West Lafayette, IN 47907, USA

Received on November 20, 2001 ; revised on March 14, 2002 and May 4, 2002 ; accepted on March 21, 2002

Motivation: We present statistical methods for determining the number of per gene replicate spots required in microarray experiments. The purpose of these methods is to obtain an estimate of the sampling variability present in microarray data, and to determine the number of replicate spots required to achieve a high probability of detecting a significant fold change in gene expression, while maintaining a low error rate. Our approach is based on data from control microarrays, and involves the use of standard statistical estimation techniques.

Results: After analyzing two experimental data sets containing control array data, we were able to determine the statistical power available for the detection of significant differential expression given differing levels of replication. The inclusion of replicate spots on microarrays not only allows more accurate estimation of the variability present in an experiment, but more importantly increases the probability of detecting genes undergoing significant fold changes in expression, while substantially decreasing the probability of observing fold changes due to chance rather than true differential expression.

Availability: The methods presented here are based on standard techniques, and are available in most statistical software packages. We used the software R to perform the computations for this work.

Contact: doerge{at}purdue.edu; blackma{at}stat.purdue.edu

* To whom correspondence should be addressed at Department of Statistics, 1399 Mathematical Sciences Building, Purdue University, West Lafayette, IN 47907-1399, USA.


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