用于肿瘤微阵列分析实验的集成微阵列表达标准化工具包（PIMENTo）流程

Pipeline for Integrated Microarray Expression Normalization Tool Kit (PIMENTo) for Tumor Microarray Profiling Experiments.

作者信息

Nash Thomas, Huff Matthew, Glen W Bailey, Hardiman Gary

机构信息

MUSC Bioinformatics, Center for Genomics Medicine, Medical University of South Carolina (MUSC), Charleston, SC, USA.

Department of Computer Science, College of Charleston, Charleston, SC, USA.

出版信息

Methods Mol Biol. 2019;1908:153-168. doi: 10.1007/978-1-4939-9004-7_11.

DOI:10.1007/978-1-4939-9004-7_11

PMID:30649727

Abstract

We have developed a Pipeline for Integrated Microarray Expression & Normalization Tool kit (PIMENTo) with the aim of streamlining the processes necessary for gene expression analysis in tumor tissue using DNA microarrays. Built with the R programming language and leveraging several open-source packages available through CRAN and Bioconductor, PIMENTo enables researchers to perform complex tasks with a minimal number of operations. Here, we describe the pipeline, review necessary data inputs, examine data outputs and quality control assessments and explore the commands to perform such analysis.

摘要

我们开发了一个集成微阵列表达与标准化工具包管道（PIMENTo），目的是简化使用DNA微阵列分析肿瘤组织中基因表达所需的流程。PIMENTo基于R编程语言构建，并利用通过CRAN和Bioconductor提供的几个开源软件包，使研究人员能够用最少的操作执行复杂任务。在此，我们描述该管道，回顾必要的数据输入，检查数据输出和质量控制评估，并探索执行此类分析的命令。