RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis
RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis
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DOI：
10.1093/bioinformatics/btl476
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发表时间：
2006-11-15
期刊：
影响因子：
5.8
通讯作者：
Chory, Joanne
中科院分区：
文献类型：
--
作者：
Hong, Fangxin;Breitling, Rainer;Chory, Joanne
虽然荟萃分析结合了来自多个研究的数据，为分析微阵列实验提供了一个强大的工具，但它提出了独特的计算挑战。生物导体包RankProd为这一目的提供了一种新的直观工具，可以在两种实验条件下检测差异表达基因。该包修改和扩展了由Breitling等人提出的秩积方法[(2004)FEBS Lett.，573，83-92]，以整合来自不同实验室和/或平台的多个微阵列研究。与基于t-检验的方法相比，它提供了几个优点，并接受来自各种平台的预处理表达数据集。检测的重要性通过非参数置换测试来评估，并且相关的P值和错误发现率(FDR)与通过用户定义的标准检测的基因一起被包括在输出中。提供可视化曲线图，以查看每个基因的实际表达水平，并进行估计的显著性测量。可用性：RankProd可在BioConductor http://www.bioconductor.org.上获得基于网络的界面将很快在http://cactus.salk.edu/RankProdContact：fhong@salk.edu.上推出。补充信息：补充数据可在生物信息学在线上获得。
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/RankProdContact: fhong@salk.eduSupplementary information: Supplementary data are available at Bioinformatics online.