Parametric Empirical Bayes Methods for Microarray Data

Assessing Differential Expression in Two-Color Microarrays: A Resampling-Based Empirical Bayes Approach

Microarrays are widely used for examining differential gene expression, identifying single nucleotide polymorphisms, and detecting methylation loci. Multiple testing methods in microarray data analysis aim at controlling both Type I and Type II error rates; however, real microarray data do not always fit their distribution assumptions. Smyth's ubiquitous parametric method, for example, inadequa...

Parametric Empirical Bayes Test and Its Application to Selection of Wavelet Threshold

In this article, we propose a new method for selecting level dependent threshold in wavelet shrinkage using the empirical Bayes framework. We employ both Bayesian and frequentist testing hypothesis instead of point estimation method. The best test yields the best prior and hence the more appropriate wavelet thresholds. The standard model functions are used to illustrate the performance of the p...

Adjusting batch effects in microarray expression data using empirical Bayes methods.

Non-biological experimental variation or "batch effects" are commonly observed across multiple batches of microarray experiments, often rendering the task of combining data from these batches difficult. The ability to combine microarray data sets is advantageous to researchers to increase statistical power to detect biological phenomena from studies where logistical considerations restrict samp...

Parametric Empirical Bayes Methods for Microarrays

A spline function approach for detecting differentially expressed genes in microarray data analysis

MOTIVATION A primary objective of microarray studies is to determine genes which are differentially expressed under various conditions. Parametric tests, such as two-sample t-tests, may be used to identify differentially expressed genes, but they require some assumptions that are not realistic for many practical problems. Non-parametric tests, such as empirical Bayes methods and mixture normal ...