normalizeCyclicLoess(limma)
normalizeCyclicLoess()所属R语言包：limma
Normalize Columns of a Matrix by Cyclic Loess
循环黄土标准化矩阵的列
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Normalize the columns of a matrix, cyclicly applying loess normalization to normalize each pair of columns to each other.
矩阵列标准化，中循环利用黄土标准化标准化每列对彼此。
用法----------Usage----------
normalizeCyclicLoess(x, weights = NULL, span=0.7, iterations = 3, method = "pairs")
参数----------Arguments----------
参数：x
numeric matrix, or object which can be coerced to a numeric matrix, containing log-expression values.
数字矩阵，或对象可以强制转换为一个数字矩阵，包含log表达式的值。
参数：weights
numeric vector of probe weights. Must be non-negative.
数字探针权重向量。必须非负。
参数：span
span of loess smoothing window, between 0 and 1.
大跨度黄土平滑窗口，0和1之间。
参数：iterations
number of times to cycle through all pairs of columns.
通过对所有列的时间周期数。
参数：method
character string specifying which variant of the cyclic loess method to use. Options are "pairs", "fast" or "affy".
字符串指定使用循环黄土方法的变种。选项"pairs"，"fast"或"affy"。
Details
详情----------Details----------
This function is intended to normalize single channel or A-value microarray intensities between arrays. Cyclic loess normalization is similar effect and intention to quantile normalization, but with some advantages, in particular the ability to incorporate probe weights.
此功能是为了规范阵列之间的单通道或A值芯片强度。循环黄土标准化位数标准化是类似的效果和意图，但具有一定优势，特别是能力纳入探针重量。
A number of variants of cylic loess have been suggested. method="pairs" implements the intuitive idea that each pair of arrays is subjected to loess normalization as for two-color arrays. This process is simply cycled through all possible pairs of arrays, then repeated for several iterations. This is the method described by Ballman et al (2004) as ordinary cyclic loess normalization.
cylic黄土变种已建议。 method="pairs"实现了直观的想法，对每个阵列两色阵列黄土标准化。这个过程是简单的循环，通过对所有可能的阵列，然后重复几个iterations。这是鲍尔曼等（2004）描述为普通循环黄土标准化的方法。
method="affy" implements a method similar to normalize.loess in the affy package, except that here we call lowess instead of loess and avoid the use of probe subsets and the predict function. In this approach, no array is modified until a complete cycle of all pairs has been completed. The adjustments are stored for a complete iteration, then averaged, and finally used to modify the arrays. The "affy" method is invariant to the order of the columns of x, whereas the "pairs" method is not. The affy approach is presumably that used by Bolstad et al (2003), although the algorithm was not explicitly described in that article.
method="affy"实现normalize.loess：中的affy的包类似的方法，除了在这里我们称之为lowess而不是loess“，避免使用探针子集和predict的功能。在这种方法中，没有数组被修改，直到所有对完整的周期已经完成。调整存储为一个完整的循环，然后取平均值，并最终用于修改数组。 "affy"方法x列的顺序是不变的，而"pairs"方法是没有的。 affy方法大概是使用由Bolstad等（2003），虽然该算法是在那篇文章中没有明确的描述。
method="fast" implements the "fast linear loess" method of Ballman et al (2004), whereby each array is simply normalized to a reference array, the reference array being the average of all the arrays. This method is relatively fast because computational time is linear in the number of arrays, whereas "pairs" and "affy" are quadratic in the number of arrays. "fast" requires n lowess fits per iteration, where n is the number of arrays, whereas "pairs" and "affy" require n*(n-1)/2 lowess fits per iteration.
method="fast"实现“快速线性黄土”鲍尔曼等人（2004年），即每个阵列简单地归到一个参考阵列，所有阵列的平均参考阵列的方法。这种方法是比较快的，因为计算时间是线性阵列的数量，而"pairs"和"affy"阵列二次。 "fast"需要列印的LOWESS适合每迭代，其中n是阵列，而"pairs"和"affy"需要N *（N-1）/ 2 LOWESS每次迭代适合。
值----------Value----------
A matrix of the same dimensions as x containing the normalized values.
矩阵x包含标准化值相同的尺寸。
作者（S）----------Author(s)----------
Yunshun (Andy) Chen and Gordon Smyth
参考文献----------References----------
Grill, DE, Oberg, AL and Therneau, TM (2004). Faster cyclic loess: normalizing RNA arrays via linear models. Bioinformatics 20, 2778-2786.
参见----------See Also----------
An overview of LIMMA functions for normalization is given in 05.Normalization.
在05.Normalization标准化LIMMA功能概述。
normalize.loess in the affy package also implements cyclic loess normalization, without weights.
normalize.loess在affy包也实现循环黄土标准化，没有重量。
转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。
注：
注1：为了方便大家学习，本文档为生物统计家园网机器人LoveR翻译而成，仅供个人R语言学习参考使用，生物统计家园保留版权。
注2：由于是机器人自动翻译，难免有不准确之处，使用时仔细对照中、英文内容进行反复理解，可以帮助R语言的学习。
注3：如遇到不准确之处，请在本贴的后面进行回帖，我们会逐渐进行修订。
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发表于 2012-2-25 23:20:01
