unifying gene expression measures from multiple platforms using factor analysis统一的基因表达措施使用因子分析从多个平台.pdfVIP

Unifying Gene Expression Measures from Multiple Platforms Using Factor Analysis 1,2 3,4 5 6 7 Xin Victoria Wang *, Roel G. W. Verhaak , Elizabeth Purdom , Paul T. Spellman , Terence P. Speed 1 Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America, 2 Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America, 3 Department of Bioinformatics and Computational Biology, MD Anderson Cancer Center, Houston, Texas, United States of America, 4 The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, United States of America, 5 Department of Statistics, University of California, Berkeley, California, United States of America, 6 Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America, 7 Bioinformatics Division, Walter Eliza Hall Institute of Medical Research, Parkville, Australia Abstract In the Cancer Genome Atlas (TCGA) project, gene expression of the same set of samples is measured multiple times on different microarray platforms. There are two main advantages to combining these measurements. First, we have the opportunity to obtain a more precise and accurate estimate of expression levels than using the individual platforms alone. Second, the combined measure simplifies downstream analysis by eliminating the need to work with three sets of expression measures and to consolidate results from the three platforms. We propose to use factor analysis (FA) to obtain a unified gene expression measure (UE) from mul