title: Fully moderated T-statistic for small sample size gene expression arrays.
abstract: Gene expression microarray experiments with few replications lead to great variability in estimates of gene variances. Several Bayesian methods have been developed to reduce this variability and to increase power. Thus far, moderated t methods assumed a constant coefficient of variation (CV) for the gene variances. We provide evidence against this assumption, and extend the method by allowing the CV to vary with gene expression. Our CV varying method, which we refer to as the fully moderated t-statistic, was compared to three other methods (ordinary t, and two moderated t predecessors). A simulation study and a familiar spike-in data set were used to assess the performance of the testing methods. The results showed that our CV varying method had higher power than the other three methods, identified a greater number of true positives in spike-in data, fit simulated data under varying assumptions very well, and in a real data set better identified higher expressing genes that were consistent with functional pathways associated with the experiments.
authors.affiliation: The Ohio State University, USA.
authors.forename: Lianbo
authors.initials: L
authors.lastname: Yu
authors.forename: Parul
authors.initials: P
authors.lastname: Gulati
authors.forename: Soledad
authors.initials: S
authors.lastname: Fernandez
authors.forename: Michael
authors.initials: M
authors.lastname: Pennell
authors.forename: Lawrence
authors.initials: L
authors.lastname: Kirschner
authors.forename: David
authors.initials: D
authors.lastname: Jarjoura
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D003198:Computer Simulation; D005189:False Positive Reactions; D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D051379:Mice; D008957:Models, Genetic; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012044:Regression Analysis; D015203:Reproducibility of Results; D018401:Sample Size; D012680:Sensitivity and Specificity