Searching for Alternative Splicing With a Joint Model on Probe Measurability and Expression Intensities

• 成果类型: Article
• 署名作者: Hu, Jianhua; He, Xuming
• 署名单位: University of Texas System; UTMD Anderson Cancer Center; University of Michigan System; University of Michigan
• 刊物名称: JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION
• ISSN/ISSBN: 0162-1459
• DOI: 10.1080/01621459.2012.682801
• 发表日期: 2012
• 页码: 935-945
• 关键词: global analysis; variants; identification; regression; aberrant; genome

摘要

The exon tiling array offers a high throughput technology to search for aberrant splicing in biomedical research, but few methods of analysis for splicing detection have been tested both statistically and empirically. Noisy measurements on nonresponsive probe selection regions and outlying intensities at some of the samples tend to distort model-based assessments. We propose a robust analysis of variance approach that incorporates an informative model on probe measurability and uses median regression rank scores for better reliability in alternative splicing detection. We study the validity and effectiveness of our proposed approach in contrast with some of the existing methods through an empirical investigation of a brain cancer experiment, where a set of biologically validated genes for splicing and nonsplicing are available. Our study demonstrates favorable performance of the proposed ranking method, but shows that analysis of statistical significance cannot be trusted from any conventional use of p-values. We warn of any routine attempt to interpret p-values and their derivatives in model-based detection of alternative splicing.