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http://hdl.handle.net/11375/22709
Title: | Comparison of Normalization Methods in Microarray Analysis |
Authors: | Yang, Rong |
Advisor: | Canty, Angelo |
Department: | Statistics |
Keywords: | normalization methods, microarray analysis, comparison, gene expression, high-density oligonucleotide, Robust Multi-chip Average |
Publication Date: | Apr-2006 |
Abstract: | <p> DNA microarrays can measure the gene expression of thousands of genes at a time to identify differentially expressed genes. The Affymetrix GeneChip system is a platform for the high-density oligonucleotide microarray to measure gene expression using hundreds of thousands of 25-mer oligonucleotide probes.</p> <p> To deal with Affymetrix microarray data, there are three stages of preprocessing to produce gene expression measurements/values. These are background correction, normalization and summarization. At each stage, numerous methods have been developed.</p> <p> Our study is based on Affymetrix MG_U74Av2 chip with 12488 probe sets. Two strains of mice called NOR and NOR.NOD_Idd4/11 mouse are hybridized for the experiment. We apply a number of commonly used and state-of-art normalization methods to the data set, thus compute the expression measurements for different methods. The major methods we discuss include Robust Multi-chip Average (RMA), MAS 5.0, GCRMA, PLIER and dChip.</p> <p> Comparisons in terms of correlation coefficient, pairwise expression measures plot, fold change and Significance Analysis of Microarray (SAM) are conducted.</p> |
URI: | http://hdl.handle.net/11375/22709 |
Appears in Collections: | Digitized Open Access Dissertations and Theses |
Files in This Item:
File | Description | Size | Format | |
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Yang_Rong_2006Apr_Masters..pdf | 3.05 MB | Adobe PDF | View/Open |
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