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Bioinformatics Advance Access published online on May 1, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn211
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© The Author (2008). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

A correction for estimating error when using the Local Pooled Error Statistical Test

Carl Murie a and Robert Nadon a,b,*

aMcGill University and Genome Quebec Innovation Centre, 740 avenue du Docteur Penfield, Montreal, Quebec, Canada, H3A 1A4 and b McGill University, Department of Human Genetics, Montreal, 1205 avenue du Docteur Penfield N5/13, Quebec, Canada, H3A 1A4

*To whom correspondence should be addressed. Dr. Robert Nadon, E-mail: robert.nadon{at}mcgill.ca


  Abstract

Jain et al. (2003) introduced the Local Pooled Error statistical test designed for use with small sample size microarray gene expression data. Based on an asymptotic proof, the test multiplicatively adjusts the standard error for a test of differences between two classes of observations by {pi}/2 due to the use of medians rather than means as measures of central tendency. The adjustment is upwardly biased at small sample sizes, however, producing fewer than expected small p-values with a consequent loss of statistical power. We present an empirical correction to the adjustment factor which removes the bias and produces theoretically expected p-values when distributional assumptions are met. Our adjusted LPE measure should prove useful to ongoing methodological studies designed to improve the LPE's performance for microarray and proteomics applications and for future work for other high-throughput biotechnologies.

Availability: The software is implemented in the R language and can be downloaded from the Bioconductor project website (http://www.bioconductor.org).

Contact: robert.nadon{at}mcgill.ca

Associate Editor: Dr. Joaquin Dopazo

Received on November 17, 2007; revised on March 28, 2008; accepted on April 24, 2008

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