{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,13]],"date-time":"2026-02-13T13:00:13Z","timestamp":1770987613691,"version":"3.50.1"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"19","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: 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\u2013control, 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.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/www.biostat.pitt.edu\/bioinfo\/software.htm<\/jats:p>\n               <jats:p>Contact: \u00a0ctseng@pitt.edu<\/jats:p>\n               <jats:p>Supplementary Information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts485","type":"journal-article","created":{"date-parts":[[2012,8,4]],"date-time":"2012-08-04T04:24:37Z","timestamp":1344054277000},"page":"2534-2536","source":"Crossref","is-referenced-by-count":170,"title":["An R package suite for microarray meta-analysis in quality control, differentially expressed gene analysis and pathway enrichment detection"],"prefix":"10.1093","volume":"28","author":[{"given":"Xingbin","family":"Wang","sequence":"first","affiliation":[{"name":"1 Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15261, USA, 2Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, 3Magee-Womens Research Institute, University of Pittsburgh, 4Department of Biostatistics, University of Pittsburgh, 5PharmaNet-i3, 224 Schilling Circle, Suite 160, Hunt Valley, MD 21031, USA, 6Department of Computational and Systems Biology, University of Pittsburgh, 7Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, 8Department of Psychiatry, University of Pittsburgh and 9Henry Ford Health System, Detroit, MI 48202, USA"}]},{"given":"Dongwan D.","family":"Kang","sequence":"additional","affiliation":[{"name":"1 Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15261, USA, 2Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, 3Magee-Womens Research Institute, University of Pittsburgh, 4Department of Biostatistics, University of Pittsburgh, 5PharmaNet-i3, 224 Schilling Circle, Suite 160, Hunt Valley, MD 21031, USA, 6Department of Computational and Systems Biology, University of Pittsburgh, 7Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, 8Department of Psychiatry, University of Pittsburgh and 9Henry Ford Health System, Detroit, MI 48202, USA"}]},{"given":"Kui","family":"Shen","sequence":"additional","affiliation":[{"name":"1 Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15261, USA, 2Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, 3Magee-Womens Research Institute, University of Pittsburgh, 4Department of Biostatistics, University of Pittsburgh, 5PharmaNet-i3, 224 Schilling Circle, Suite 160, Hunt Valley, MD 21031, USA, 6Department of Computational and Systems Biology, University of Pittsburgh, 7Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, 8Department of Psychiatry, University of Pittsburgh and 9Henry Ford Health System, Detroit, MI 48202, USA"}]},{"given":"Chi","family":"Song","sequence":"additional","affiliation":[{"name":"1 Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15261, USA, 2Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, 3Magee-Womens Research Institute, University of Pittsburgh, 4Department of Biostatistics, University of Pittsburgh, 5PharmaNet-i3, 224 Schilling Circle, Suite 160, Hunt Valley, MD 21031, USA, 6Department of Computational and Systems Biology, University of Pittsburgh, 7Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, 8Department of Psychiatry, University of Pittsburgh and 9Henry Ford Health System, Detroit, MI 48202, USA"}]},{"given":"Shuya","family":"Lu","sequence":"additional","affiliation":[{"name":"1 Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15261, USA, 2Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, 3Magee-Womens Research Institute, University of Pittsburgh, 4Department of Biostatistics, University of Pittsburgh, 5PharmaNet-i3, 224 Schilling Circle, Suite 160, Hunt Valley, MD 21031, USA, 6Department of Computational and Systems Biology, University of Pittsburgh, 7Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, 8Department of Psychiatry, University of Pittsburgh and 9Henry Ford Health System, Detroit, MI 48202, USA"}]},{"given":"Lun-Ching","family":"Chang","sequence":"additional","affiliation":[{"name":"1 Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15261, USA, 2Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, 3Magee-Womens Research Institute, University of Pittsburgh, 4Department of Biostatistics, University of Pittsburgh, 5PharmaNet-i3, 224 Schilling Circle, Suite 160, Hunt Valley, MD 21031, USA, 6Department of Computational and Systems Biology, University of Pittsburgh, 7Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, 8Department of Psychiatry, University of Pittsburgh and 9Henry Ford Health System, Detroit, MI 48202, USA"}]},{"given":"Serena G.","family":"Liao","sequence":"additional","affiliation":[{"name":"1 Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15261, USA, 2Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, 3Magee-Womens Research Institute, University of Pittsburgh, 4Department of Biostatistics, University of Pittsburgh, 5PharmaNet-i3, 224 Schilling Circle, Suite 160, Hunt Valley, MD 21031, USA, 6Department of Computational and Systems Biology, University of Pittsburgh, 7Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, 8Department of Psychiatry, University of Pittsburgh and 9Henry Ford Health System, Detroit, MI 48202, USA"}]},{"given":"Zhiguang","family":"Huo","sequence":"additional","affiliation":[{"name":"1 Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15261, USA, 2Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, 3Magee-Womens Research Institute, University of Pittsburgh, 4Department of Biostatistics, University of Pittsburgh, 5PharmaNet-i3, 224 Schilling Circle, Suite 160, Hunt Valley, MD 21031, USA, 6Department of Computational and Systems Biology, University of Pittsburgh, 7Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, 8Department of Psychiatry, University of Pittsburgh and 9Henry Ford Health System, Detroit, MI 48202, USA"}]},{"given":"Shaowu","family":"Tang","sequence":"additional","affiliation":[{"name":"1 Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15261, USA, 2Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, 3Magee-Womens Research Institute, University of Pittsburgh, 4Department of Biostatistics, University of Pittsburgh, 5PharmaNet-i3, 224 Schilling Circle, Suite 160, Hunt Valley, MD 21031, USA, 6Department of Computational and Systems Biology, University of Pittsburgh, 7Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, 8Department of Psychiatry, University of Pittsburgh and 9Henry Ford Health System, Detroit, MI 48202, USA"}]},{"given":"Ying","family":"Ding","sequence":"additional","affiliation":[{"name":"1 Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15261, USA, 2Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, 3Magee-Womens Research Institute, University of Pittsburgh, 4Department of Biostatistics, University of Pittsburgh, 5PharmaNet-i3, 224 Schilling Circle, Suite 160, Hunt Valley, MD 21031, USA, 6Department of Computational and Systems Biology, University of Pittsburgh, 7Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, 8Department of Psychiatry, University of Pittsburgh and 9Henry Ford Health System, Detroit, MI 48202, USA"}]},{"given":"Naftali","family":"Kaminski","sequence":"additional","affiliation":[{"name":"1 Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15261, USA, 2Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, 3Magee-Womens Research Institute, University of Pittsburgh, 4Department of Biostatistics, University of Pittsburgh, 5PharmaNet-i3, 224 Schilling Circle, Suite 160, Hunt Valley, MD 21031, USA, 6Department of Computational and Systems Biology, University of Pittsburgh, 7Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, 8Department of Psychiatry, University of Pittsburgh and 9Henry Ford Health System, Detroit, MI 48202, USA"}]},{"given":"Etienne","family":"Sibille","sequence":"additional","affiliation":[{"name":"1 Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15261, USA, 2Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, 3Magee-Womens Research Institute, University of Pittsburgh, 4Department of Biostatistics, University of Pittsburgh, 5PharmaNet-i3, 224 Schilling Circle, Suite 160, Hunt Valley, MD 21031, USA, 6Department of Computational and Systems Biology, University of Pittsburgh, 7Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, 8Department of Psychiatry, University of Pittsburgh and 9Henry Ford Health System, Detroit, MI 48202, USA"}]},{"given":"Yan","family":"Lin","sequence":"additional","affiliation":[{"name":"1 Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15261, USA, 2Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, 3Magee-Womens Research Institute, University of Pittsburgh, 4Department of Biostatistics, University of Pittsburgh, 5PharmaNet-i3, 224 Schilling Circle, Suite 160, Hunt Valley, MD 21031, USA, 6Department of Computational and Systems Biology, University of Pittsburgh, 7Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, 8Department of Psychiatry, University of Pittsburgh and 9Henry Ford Health System, Detroit, MI 48202, USA"}]},{"given":"Jia","family":"Li","sequence":"additional","affiliation":[{"name":"1 Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15261, USA, 2Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, 3Magee-Womens Research Institute, University of Pittsburgh, 4Department of Biostatistics, University of Pittsburgh, 5PharmaNet-i3, 224 Schilling Circle, Suite 160, Hunt Valley, MD 21031, USA, 6Department of Computational and Systems Biology, University of Pittsburgh, 7Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, 8Department of Psychiatry, University of Pittsburgh and 9Henry Ford Health System, Detroit, MI 48202, USA"}]},{"given":"George C.","family":"Tseng","sequence":"additional","affiliation":[{"name":"1 Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15261, USA, 2Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, 3Magee-Womens Research Institute, University of Pittsburgh, 4Department of Biostatistics, University of Pittsburgh, 5PharmaNet-i3, 224 Schilling Circle, Suite 160, Hunt Valley, MD 21031, USA, 6Department of Computational and Systems Biology, University of Pittsburgh, 7Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, 8Department of Psychiatry, University of Pittsburgh and 9Henry Ford Health System, Detroit, MI 48202, USA"},{"name":"1 Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15261, USA, 2Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, 3Magee-Womens Research Institute, University of Pittsburgh, 4Department of Biostatistics, University of Pittsburgh, 5PharmaNet-i3, 224 Schilling Circle, Suite 160, Hunt Valley, MD 21031, USA, 6Department of Computational and Systems Biology, University of Pittsburgh, 7Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, 8Department of Psychiatry, University of Pittsburgh and 9Henry Ford Health System, Detroit, MI 48202, USA"}]}],"member":"286","published-online":{"date-parts":[[2012,8,3]]},"reference":[{"key":"2023012513141346900_bts485-B1","doi-asserted-by":"crossref","first-page":"i84","DOI":"10.1093\/bioinformatics\/btg1010","article-title":"Combining multiple microarray studies and modeling interstudy variation","volume":"19","author":"Choi","year":"2003","journal-title":"Bioinformatics"},{"key":"2023012513141346900_bts485-B2","doi-asserted-by":"crossref","first-page":"2825","DOI":"10.1093\/bioinformatics\/btl476","article-title":"RankProd: a bioconductor package for detecting differentially expressed genes in 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