Use of signal quality measurements to gain efficiency in the analysis of cDNA microarray data

作     者：Tracy L Bergemann 

作者机构：Division of BiostatisticsUniversity of Minnesota 

出 版 物：《Journal of Genetics and Genomics》 (遗传学报（英文版）)

年 卷 期：2010年第37卷第4期

页      面：265-279页

核心收录：

学科分类：0710[理学-生物学] 07[理学] 08[工学] 09[农学] 071007[理学-遗传学] 0901[农学-作物学] 0836[工学-生物工程] 090102[农学-作物遗传育种] 

主　　题：microarrays signal quality prediction measurement error models 

摘      要：This research provides a new way to measure error in microarray data in order to improve gene expression analysis. Microarray data contains many sources of error. In order to glean information about mRNA expression levels, the true signal must first be segregated from noise. This research focuses on the variation that can be captured at the spot level in cDNA microarray images. Variation at other levels, due to differences at the array, dye, and block levels, can be corrected for by a variety of existing normalization procedures. Two signal quality estimates that capture the reliability of each spot printed on a microarray are described. A parametric estimate of within-spot vari ance, referred to here as σ^2spot, assumes that pixels follow a normal distribution and are spatially correlated. A non-parametric estimate of error, called the mean square prediction error （MSPE）, assumes that spots of high quality possess pixels that are similar to their neighbors. This paper will provide a framework to use either spot quality measure in downstream analysis, specifically as weights in regression models. Using these spot quality estimates as weights can result in greater efficiency, in a statistical sense, when modeling mi- croarray data.