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

• DOI: 10.1093/bioinformatics/btn211
• Publication Date: 2008-05-04T04:47:30Z
• Authors: Carl Murie; Robert Nadon
• Keywords: 0301 basic medicine; 03 medical and health sciences; Data Interpretation, Statistical; Gene Expression Profiling; Reproducibility of Results; Artifacts; Sensitivity and Specificity; Algorithms; Oligonucleotide Array Sequence Analysis

Abstract Jain et al. introduced the Local Pooled Error (LPE) 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 π/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: [e-mail]