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Activity Number: 102
Type: Contributed
Date/Time: Monday, July 30, 2007 : 8:30 AM to 10:20 AM
Sponsor: Biometrics Section
Abstract - #310010
Title: Microarray Gene Expression Analysis of Soybean Genome Using R-Bioconductor
Author(s): Jean Roayaei*+
Companies: National Institutes of Health
Address: Room 28, Miller Drive Frederick, MD, 21702,
Keywords: microarray ; gene expression ; Affymetrix GeneChip ; quality control of chips ; empirical Bayes t ; volcano plot
Abstract:

A popular application of microarray technology is the identification of genes that are differentially expressed in two different populations. With Affymetrix GeneChip technology, numerous steps are required in first, establishing the quality control of chips, and, second, in selecting interesting genes. Due to the cost involved in Affymetrix microarray technology, experiments using small numbers of arrays are common. In this research, we processed three Hawaii/Ressitent and three Taiwan/Susceptible arrays. This paper describes specific procedures for (1) conducting quality assessment of Affymetrix GeneChip soybean genome data and (2) performing analyses to determine differential gene expression using Bioconductor and R. All biostatistical analyses performed in this research were conducted using R version 2.4.0 and Bioconductor version 1.9.

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Revised September, 2007