Author

Mark Dane

Date

6-2014

Document Type

Thesis

Degree Name

M.S.

Department

Department of Medical Informatics and Clinical Epidemiology

Institution

Oregon Health & Science University

Abstract

Cellular microarrays are a combination of well plate and microarray technologies that create an efficient high-throughput method to quantitate the phenotypes of cells in response to perturbations such as microenvironments, RNAi and drugs. This thesis covers the development and use of an extensible computational pipeline to process High Content Screening data from cellular microarrays. Extensive Exploratory Data Analysis is performed to identify technical variations and inform normalizations that filter for biological variations. Robust rank product scoring combines replicate and channel data to prioritize hits for different biological questions. The pipeline has been applied to Cell Spot Microarrays and MEArray datasets, uncovering experiment design issues and generating hit lists for validation. A method to generate simulated datasets with variations that mimic those in actual microarrays has been developed and used to optimize the pipeline and predict the results for different experiment designs.

Identifier

doi:10.6083/M43R0RMH

School

School of Medicine

Available for download on Tuesday, June 27, 2017

Share

COinS