Analysis of variance for gene expression microarray data：（基因表达微阵列数据的方差分析）.pdfVIP

JOURNAL OF COMPUTATIONAL BIOLOGY Volume 7, Number 6, 2000 Mary Ann Liebert, Inc. Pp. 819–837 Analysis of Variance for Gene Expression Microarray Data M. KATHLEEN KERR,1 MITCHELL MARTIN,2 and GARY A. CHURCHILL 1 ABSTRACT Spotted cDNA microarrays are emerging as a powerful and cost-effective tool for large- scale analysis of gene expression. Microarrays can be used to measure the relative quantities of speci c mRNAs in two or more tissue samples for thousands of genes simultaneously. While the power of this technology has been recognized, many open questions remain about appropriate analysis of microarray data. One question is how to make valid estimates of the relative expression for genes that are not biased by ancillary sources of variation. Recognizing that there is inherent “ noise” in microarray data, how does one estimate the error variation associated with an estimated change in expression, i.e., how does one construct the error bars? We demonstrate that ANOVA methods can be used to normalize microarray data and provide estimates of changes in gene expression that are corrected for potential confounding effects. This approach establishes a framework for the general analysis and interpretation of microarray data. Key words: Gene expression microarray, differential expression, analysis of variance, bootstrap. INTRODUCTION he regulation of gene expression in a cell begins at the level of transcription of DNA into TmRNA. Although subsequent processes such as differential degradation of mRNA in the cytoplasm and differential translation also regulate the expression of genes, it is of great interest to estimate the relative quantities of mRNA species in populat