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


BACKGROUND
The software is implemented in the R language and can be downloaded from the Bioconductor project website (http://www.bioconductor.org).
Murie
Carl
C
McGill University and Genome Quebec Innovation Centre, 740 avenue du Docteur Penfield, Montreal, Quebec, Canada.
Nadon
Robert
R
D000465:Algorithms; D016477:Artifacts; D003627:Data Interpretation, Statistical; D020869:Gene Expression Profiling / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity