05.Normalization(limma)
05.Normalization()所属R语言包：limma
Normalization of Microarray Data
微阵列数据的标准化
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This page gives an overview of the LIMMA functions available to normalize data from single-channel or two-colour microarrays. Smyth and Speed (2003) give an overview of the normalization techniques implemented in the functions for two-colour arrays.
这页给出了一个概述的LIMMA功能，可从单声道或两色芯片的数据标准化。史密斯和速度（2003年）两色阵列功能实现标准化技术概述。
Usually data from spotted microarrays will be normalized using normalizeWithinArrays. A minority of data will also be normalized using normalizeBetweenArrays if diagnostic plots suggest a difference in scale between the arrays.
一般斑点芯片的数据将标准化使用normalizeWithinArrays。少数数据也将归使用normalizeBetweenArrays如果诊断图表明，在大规模的阵列之间的差异。
In rare circumstances, data might be normalized using normalizeForPrintorder before using normalizeWithinArrays.
在罕见的情况下，数据可能会标准化使用normalizeForPrintorder用normalizeWithinArrays前。
All the normalization routines take account of spot quality weights which might be set in the data objects. The weights can be temporarily modified using modifyWeights to, for example, remove ratio control spots from the normalization process.
所有的标准化例程采取现场质量设置权重，可能会在数据对象的帐户。使用modifyWeights，例如，从标准化的进程比控制点的权重，可以暂时修改。
If one is planning analysis of single-channel information from the microarrays rather than analysis of differential expression based on log-ratios, then the data should be normalized using a single channel-normalization technique. Single channel normalization uses further options of the normalizeBetweenArrays function. For more details see the LIMMA User's Guide which includes a section on single-channel normalization.
如果一个单声道的芯片，而不是基于对数比率的差异表达分析信息分析，然后将数据应使用单一通道标准化技术标准化。单通道标准化使用normalizeBetweenArrays函数的进一步选择。详细内容见的LIMMA用户指南，其中包括第一个单声道标准化。
normalizeWithinArrays uses utility functions MA.RG, loessFit and normalizeRobustSpline.
normalizeWithinArrays使用实用功能MA.RG，loessFit和normalizeRobustSpline。
normalizeBetweenArrays is the main normalization function for one-channel arrays, as well as an optional function for two-colour arrays. normalizeBetweenArrays uses utility functions normalizeMedianAbsValues, normalizeMedianAbsValues, normalizeQuantiles and normalizeCyclicLoess, none of which need to be called directly by users.
normalizeBetweenArrays是一个通道阵列，以及两色阵列的可选功能的主要标准化的功能。 normalizeBetweenArrays使用实用功能normalizeMedianAbsValues，normalizeMedianAbsValues，normalizeQuantiles和normalizeCyclicLoess，其中需要由用户直接调用。
The function normalizeVSN is also provided as a interface to the vsn package. It performs variance stabilizing normalization, an algorithm which includes background correction, within and between normalization together, and therefore doesn't fit into the paradigm of the other methods.
功能normalizeVSN还提供作为一个VSN包的接口。它执行方差稳定的标准化，其中包括背景校正，内部和之间的标准化，因此不适合其他方法范式的算法。
removeBatchEffect can be used to remove a batch effect, associated with hybridization time or some other technical variable, prior to unsupervised analysis.
removeBatchEffect可用于消除批次效应，杂交时间或其他一些技术变量，事先无监督分析。
作者（S）----------Author(s)----------
Gordon Smyth
参考文献----------References----------
Methods 31, 265-273. http://www.statsci.org/smyth/pubs/normalize.pdf
转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。
注：
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发表于 2012-2-25 23:08:44
