RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis

被引:571
作者
Hong, Fangxin [1 ]
Breitling, Rainer
McEntee, Connor W.
Wittner, Ben S.
Nemhauser, Jennifer L.
Chory, Joanne
机构
[1] Salk Inst Biol Studies, Plant Biol Lab, La Jolla, CA USA
[2] Salk Inst Biol Studies, Howard Hughes Med Inst, La Jolla, CA USA
[3] Univ Groningen, Groningen Bioinformat Ctr, Haren, Netherlands
[4] Massachusetts Gen Hosp, Ctr Canc Res, Boston, MA 02114 USA
[5] Univ Washington, Dept Biol, Seattle, WA 98195 USA
基金
美国国家科学基金会;
关键词
D O I
10.1093/bioinformatics/btl476
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
While meta-analysis provides a powerful tool for analyzing microarray experiments by combining data from multiple studies, it presents unique computational challenges. The Bioconductor package RankProd provides a new and intuitive tool for this purpose in detecting differentially expressed genes under two experimental conditions. The package modifies and extends the rank product method proposed by Breitling et al., [(2004) FEBS Lett., 573, 83-92] to integrate multiple microarray studies from different laboratories and/or platforms. It offers several advantages over t-test based methods and accepts pre-processed expression datasets produced from a wide variety of platforms. The significance of the detection is assessed by a non-parametric permutation test, and the associated P-value and false discovery rate (FDR) are included in the output alongside the genes that are detected by user-defined criteria. A visualization plot is provided to view actual expression levels for each gene with estimated significance measurements. Availability: RankProd is available at Bioconductor http://www.bioconductor.org. A web-based interface will soon be available at http://cactus.salk.edu/RankProd Contact: fhong@salk.edu Supplementary information: Supplementary data are available at Bioinformatics online.
引用
收藏
页码:2825 / 2827
页数:3
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