A calibration model for Affymetrix GeneChip data analysis
Date Issued
2006
Date
2006
Author(s)
Chen, Tai-Shen
DOI
zh-TW
Abstract
Affymetrix high-density oligonucleotide biochips have been widely used in various biological and medical experiments. One of the important processes in analysis of such experimental data is to summarize the probe intensities corresponding to a unigene into a single gene expression value. The gene expression value obtained from different summarization methods can lead to controversy results in identification of differentially expressed genes, and in further analyses such as clustering analysis and gene network analysis. In this study, we propose a new summarization method to obtain gene expression values based on a modified calibration model presented in Rocke and Durbin (2001), which is originally used to analyze the data of gene level. We adapt it for the data of probe level. The proposed method could compete with some existing methods (RMA, MBEI, MAS5.0) according to the results of analyzing a spike-in data set provided by Affymetrix. Furthermore, we develop a simulation mechanism to mimic naturally occurring data based on the modified calibration model. Finally, we offer a method of determining the sample size for the test-control experiment using Affymetrix GeneChips.
Subjects
生物晶片
資料分析
校準模式
Affymetrix
microarray
calibration model
Type
thesis
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