ArrayPipe: a flexible processing pipeline for microarray data
ArrayPipe: a flexible processing pipeline for microarray data
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DOI：
10.1093/nar/gkh446
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发表时间：
2004-07-01
影响因子：
14.9
通讯作者：
Brinkman, FSL
中科院分区：
文献类型：
--
作者：
Hokamp, K;Roche, FM;Brinkman, FSL
一些微阵列分析软件包已经存在，但是，没有一个结合了用户友好的功能，基于网络的界面与潜在的能力，分析多个阵列一次使用灵活的分析步骤。ArrayPipe网络服务器（可在www.pathogenomics.ca/arraypipe免费获得）允许将复杂分析自动应用于微阵列数据，其范围可以从单个载玻片到大型数据集，包括重复和染料交换。它处理最常用的双标记阵列定量软件包的输出。应用功能范围从载玻片的质量评估到各种数据可视化，再到多步分析，包括标准化、差异表达基因的检测以及基因列表的比较和突出显示。高度可定制的操作设置有助于不受限制地安排功能，这些功能可以存储为操作配置文件。基于Web的功能和命令行功能的独特组合实现了舒适的流程配置，可以重复应用于高吞吐量的大型数据集。输出包括格式化为标准网页的报告和可以插入到其他分析程序中的制表符分隔的计算值列表。其他功能，如基于Web的电子表格功能，自动并行化和密码保护，使其成为个人和大型团体的微阵列研究中的强大工具。
A number of microarray analysis software packages exist already; however, none combines the user-friendly features of a web-based interface with potential ability to analyse multiple arrays at once using flexible analysis steps. The ArrayPipe web server (freely available at www.pathogenomics.ca/arraypipe) allows the automated application of complex analyses to microarray data which can range from single slides to large data sets including replicates and dye-swaps. It handles output from most commonly used quantification software packages for dual-labelled arrays. Application features range from quality assessment of slides through various data visualizations to multi-step analyses including normalization, detection of differentially expressed genes, andcomparison and highlighting of gene lists. A highly customizable action set-up facilitates unrestricted arrangement of functions, which can be stored as action profiles. A unique combination of web-based and command-line functionality enables comfortable configuration of processes that can be repeatedly applied to large data sets in high throughput. The output consists of reports formatted as standard web pages and tab-delimited lists of calculated values that can be inserted into other analysis programs. Additional features, such as web-based spreadsheet functionality, auto-parallelization and password protection make this a powerful tool in microarray research for individuals and large groups alike.