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ANALYSIS OF ROBUSTNESS AND RESIDUALS IN THE AFFYMETRIX
GENE EXPRESSION MICROARRAY SUMMARIZATION
by
Huanying Ge
A Dissertation Presented to the
FACULTY OF THE GRADUATE SCHOOL
UNIVERSITY OF SOUTHERN CALIFORNIA
In Partial Fulfillment of the
Requirements for the Degree
MASTER OF SCIENCE
(STATISTICS)
August 2008
Copyright 2008 Huanying Ge
Object Description
| Title | Analysis of robustness and residuals in the Affymetrix gene expression microarray summarization |
| Author | Ge, Huanying |
| Author email | hge@usc.edu |
| Degree | Master of Science |
| Document type | Thesis |
| Degree program | Statistics |
| School | College of Letters, Arts and Sciences |
| Date defended/completed | 2008-07-01 |
| Date submitted | 2008 |
| Restricted until | Restricted until 19 June 2010. |
| Date published | 2010-06-19 |
| Advisor (committee chair) | Li, Lei M. |
| Advisor (committee member) |
Goldstein, Larry M. Chen, Liang |
| Abstract | DNA microarray has been widely used in the field of functional genomics. The estimation of gene expression from microarray is a statistical problem where a lot of effort has been made. In this study, we focus on the summarization step of Affymetrix microarray pre-processing. We apply the Least Absolute Deviation (LAD) regression to estimate the probe- and treatment-specific effect in the widely-taken two-factor model. The median polish can be used as an approximation approach for the LAD regression in this two-factor summarization model. We show that the LAD estimator is robust in the sense that it has bounded influence where the bound is strongly associated with the RNA concentration. Furthermore, we calculate the influence bound and standard error which are used as the measure of accuracy for the log-ratio estimate. |
| Keyword | LAD; microarray; robustness |
| Language | English |
| Part of collection | University of Southern California dissertations and theses |
| Publisher (of the original version) | University of Southern California |
| Place of publication (of the original version) | Los Angeles, California |
| Publisher (of the digital version) | University of Southern California. Libraries |
| Type | texts |
| Legacy record ID | usctheses-m1278 |
| Contributing entity | University of Southern California |
| Rights | Ge, Huanying |
| Repository name | Libraries, University of Southern California |
| Repository address | Los Angeles, California |
| Repository email | cisadmin@dots.usc.edu |
| Filename | etd-Ge-20080619 |
| Archival file | uscthesesreloadpub_Volume32/etd-Ge-20080619.pdf |
Description
| Title | Page 1 |
| Contributing entity | University of Southern California |
| Repository email | cisadmin@dots.usc.edu |
| Full text | ANALYSIS OF ROBUSTNESS AND RESIDUALS IN THE AFFYMETRIX GENE EXPRESSION MICROARRAY SUMMARIZATION by Huanying Ge A Dissertation Presented to the FACULTY OF THE GRADUATE SCHOOL UNIVERSITY OF SOUTHERN CALIFORNIA In Partial Fulfillment of the Requirements for the Degree MASTER OF SCIENCE (STATISTICS) August 2008 Copyright 2008 Huanying Ge |
