title: An R package suite for microarray meta-analysis in quality control, differentially expressed gene analysis and pathway enrichment detection.
abstract: CONCLUSIONS
  With the rapid advances and prevalence of high-throughput genomic technologies, integrating information of multiple relevant genomic studies has brought new challenges. Microarray meta-analysis has become a frequently used tool in biomedical research. Little effort, however, has been made to develop a systematic pipeline and user-friendly software. In this article, we present MetaOmics, a suite of three R packages MetaQC, MetaDE and MetaPath, for quality control, differentially expressed gene identification and enriched pathway detection for microarray meta-analysis. MetaQC provides a quantitative and objective tool to assist study inclusion/exclusion criteria for meta-analysis. MetaDE and MetaPath were developed for candidate marker and pathway detection, which provide choices of marker detection, meta-analysis and pathway analysis methods. The system allows flexible input of experimental data, clinical outcome (case-control, multi-class, continuous or survival) and pathway databases. It allows missing values in experimental data and utilizes multi-core parallel computing for fast implementation. It generates informative summary output and visualization plots, operates on different operation systems and can be expanded to include new algorithms or combine different types of genomic data. This software suite provides a comprehensive tool to conveniently implement and compare various genomic meta-analysis pipelines.
  
  
  BACKGROUND
  http://www.biostat.pitt.edu/bioinfo/software.htm
  
  
  BACKGROUND
  ctseng@pitt.edu
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15261, USA.
authors.forename: Xingbin
authors.initials: X
authors.lastname: Wang
authors.forename: Dongwan D
authors.initials: DD
authors.lastname: Kang
authors.forename: Kui
authors.initials: K
authors.lastname: Shen
authors.forename: Chi
authors.initials: C
authors.lastname: Song
authors.forename: Shuya
authors.initials: S
authors.lastname: Lu
authors.forename: Lun-Ching
authors.initials: LC
authors.lastname: Chang
authors.forename: Serena G
authors.initials: SG
authors.lastname: Liao
authors.forename: Zhiguang
authors.initials: Z
authors.lastname: Huo
authors.forename: Shaowu
authors.initials: S
authors.lastname: Tang
authors.forename: Ying
authors.initials: Y
authors.lastname: Ding
authors.forename: Naftali
authors.initials: N
authors.lastname: Kaminski
authors.forename: Etienne
authors.initials: E
authors.lastname: Sibille
authors.forename: Yan
authors.initials: Y
authors.lastname: Lin
authors.forename: Jia
authors.initials: J
authors.lastname: Li
authors.forename: George C
authors.initials: GC
authors.lastname: Tseng
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods; D020869:Gene Expression Profiling / Q000379:methods*; D023281:Genomics / Q000379:methods*; D006801:Humans; D008297:Male; D015201:Meta-Analysis as Topic; D046228:Microarray Analysis / Q000379:methods*; D011471:Prostatic Neoplasms / Q000235:genetics; D011786:Quality Control; D012984:Software