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High-Throughput Data Analysis: Application To Micronuclei Frequency And T-Cell Receptor Sequencing, Mateusz Makowski

Theses and Dissertations

The advent of high-throughput sequencing has brought about the creation of an unprecedented amount of research data. Analytical methodology has not been able to keep pace with the plethora of data being produced. Two assays, ImmunoSEQ and the cytokinesisblock micronucleus (CBMN), that both produce count data and have few methods available to analyze them are considered.

ImmunoSEQ is a sequencing assay that measures the beta T-cell receptor (TCR) repertoire. The ImmunoSEQ assay was used to describe the TCR repertoires of patients that have undergone hematopoietic stem cell transplantation (HSCT). Several different methods for spectratype analysis were extended to the TCR …

Stereotype Logit Models For High Dimensional Data, Andre Williams

Theses and Dissertations

Gene expression studies are of growing importance in the field of medicine. In fact, subtypes within the same disease have been shown to have differing gene expression profiles (Golub et al., 1999). Often, researchers are interested in differentiating a disease by a categorical classification indicative of disease progression. For example, it may be of interest to identify genes that are associated with progression and to accurately predict the state of progression using gene expression data. One challenge when modeling microarray gene expression data is that there are more genes (variables) than there are observations. In addition, the genes usually demonstrate …

Sensitivity To Distributional Assumptions In Estimation Of The Odp Thresholding Function, Wendy Jill Bunn

Theses and Dissertations

Recent technological advances in fields like medicine and genomics have produced high-dimensional data sets and a challenge to correctly interpret experimental results. The Optimal Discovery Procedure (ODP) (Storey 2005) builds on the framework of Neyman-Pearson hypothesis testing to optimally test thousands of hypotheses simultaneously. The method relies on the assumption of normally distributed data; however, many applications of this method will violate this assumption. This thesis investigates the sensitivity of this method to detection of significant but nonnormal data. Overall, estimation of the ODP with the method described in this thesis is satisfactory, except when the nonnormal alternative distribution has …

A Simulation-Based Approach For Evaluating Gene Expression Analyses, Carly Ruth Pendleton

Theses and Dissertations

Microarrays enable biologists to measure differences in gene expression in thousands of genes simultaneously. The data produced by microarrays present a statistical challenge, one which has been met both by new modifications of existing methods and by completely new approaches. One of the difficulties with a new approach to microarray analysis is validating the method's power and sensitivity. A simulation study could provide such validation by simulating gene expression data and investigating the method's response to changes in the data; however, due to the complex dependencies and interactions found in gene expression data, such a simulation would be complicated and …