Year: 2009 Author: E. Shannon Neeley, PhD Advisor: Keith A. Baggerly Committee Members: Rudy Guerra, Marek Kimmel, Michael Gustin Thesis Title: Models for the Preprocessing of Reverse Phase Protein Arrays Abstract: Reverse-phase protein arrays (RPPA) are important tools for the analysis of proteins in biological systems. RPPAs combine traditional assays for measuring proteins with microarray technology. Importance of data preprocessing for other microarray formats has been shown. Many of the same issues carry over to RPPAs, but have not been dealt with as extensively. We develop models for the processing of RPPA data. Most notably, a normalization model is introduced that corrects for sample loading while accounting for the fact that expression estimates are computed separately for each array. Results show that this model recovers true structure better than standard methods.