Genetics and Genomics Commons^™

Comparison Of Software Packages For Detecting Differentially Expressed Genes From Single-Sample Rna-Seq Data, Rong Zhou

Electronic Theses and Dissertations

RNA-sequencing (RNA-seq) has rapidly become the tool in many genome-wide transcriptomic studies. It provides a way to understand the RNA environment of cells in different physiological or pathological states to determine how cells respond to these changes. RNA-seq provides quantitative information about the abundance of different RNA species present in a given sample. If the difference or change observed in the read counts or expression level between two experimental conditions is statistically significant, the gene is declared as differentially expressed. A large number of methods for detecting differentially expressed genes (DEGs) with RNA-seq have been developed, such as the methods …

Multiple Testing Correction With Repeated Correlated Outcomes: Applications To Epigenetics, Katie Leap

Masters Theses

Epigenetic changes (specifically DNA methylation) have been associated with adverse health outcomes; however, unlike genetic markers that are fixed over the lifetime of an individual, methylation can change. Given that there are a large number of methylation sites, measuring them repeatedly introduces multiple testing problems beyond those that exist in a static genetic context. Using simulations of epigenetic data, we considered different methods of controlling the false discovery rate. We considered several underlying associations between an exposure and methylation over time.

We found that testing each site with a linear mixed effects model and then controlling the false discovery rate …