limmaGUI: A graphical user interface for linear modeling of microarray data
limmaGUI: A graphical user interface for linear modeling of microarray data
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DOI：
10.1093/bioinformatics/bth449
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发表时间：
2004-12-12
期刊：
影响因子：
5.8
通讯作者：
Smyth, GK
中科院分区：
文献类型：
--
作者：
Wettenhall, JM;Smyth, GK
limmaGUI是一个基于R - Tcl/Tk的图形用户界面（GUI），用于对双色斑点微阵列实验的数据进行探索和线性建模，特别是对复杂实验中差异表达的评估。limmaGUI为R语言的limma包中的统计方法提供了一个接口，其本身也是作为一个R包来实现的。该软件提供了点击式访问一系列用于微阵列数据的背景校正、图形显示、归一化和分析的方法。使用线性模型和对比，可以处理涉及多种RNA来源的任意复杂的微阵列实验。提供了基因水平残差方差的经验贝叶斯收缩，以确保即使在阵列数量较少时也能得到稳定的结果。为定量斑点质量权重、对照斑点、阵列内重复斑点和多重检验提供了集成支持。limmaGUI可用于运行R的大多数平台，包括Windows、Mac和大多数类Unix系统。
limmaGUI is a graphical user interface (GUI) based on R-Tcl/Tk for the exploration and linear modeling of data from two-color spotted microarray experiments, especially the assessment of differential expression in complex experiments. limmaGUI provides an interface to the statistical methods of the limma package for R, and is itself implemented as an R package. The software provides point and click access to a range of methods for background correction, graphical display, normalization, and analysis of microarray data. Arbitrarily complex microarray experiments involving multiple RNA sources can be accomodated using linear models and contrasts. Empirical Bayes shrinkage of the gene-wise residual variances is provided to ensure stable results even when the number of arrays is small. Integrated support is provided for quantitative spot quality weights, control spots, within-array replicate spots and multiple testing. limmaGUI is available for most platforms on the which R runs including Windows, Mac and most flavors of Unix.