Detecting differentially expressed genes in heterogeneous diseases using half Student’s t-test

Detecting Differentially Expressed Genes in Microarrays Using Bayesian Model Selection

DNA microarrays open up a broad new horizon for investigators interested in studying the genetic determinants of disease. The high throughputnature of these arrays, where differential expression for thousands of genes can bemeasured simultaneously, creates an enormous wealth of information, but also poses a challenge for data analysis because of the large multiple testing problem involved. The ...

Detecting Differentially Expressed Genes Using Calibrated Bayes Factors

A common interest in microarray data analysis is to identify genes having changes in expression values between different biological conditions. The existing methods include using two-sample t-statistics, modified t-statistics (SAM), Bayesian t-statistics (Cyber-T), semiparametric hierarchical Bayesian models, and nonparametric permutation tests. All these methods essentially compare two populat...

Description of Logit-t: Detecting Differentially Expressed Genes Using Probe-Level Data

Detecting differentially expressed genes in longitudinal microarray experiments

In this work we propose a statistical approach for the detection of differentially expressed genes. Specifically, we envisage a longitudinal study design where multiple biological replicates are available and each individual is observed at more than one time point. We present a semi-parametric random effects model based on smoothing splines and introduce a visual-distance metric for detecting t...

Sample size for detecting differentially expressed genes in microarray experiments

Background: Microarray experiments are often performed with a small number of biological replicates, resulting in low statistical power for detecting differentially expressed genes and concomitant high false positive rates. While increasing sample size can increase statistical power and decrease error rates, with too many samples, valuable resources are not used efficiently. The issue of how ma...