normalizePlates(cellHTS)
normalizePlates()所属R语言包：cellHTS
Plate-wise data normalization, and data transformation
板明智的标准化数据，数据转换
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Normalization of the data xraw in a cellHTS object. This is done separately for each plate, replicate and channel. Optionally, a data transformation such as log, and a transformation to z-scores can be performed.
数据标准化xraw在cellHTS对象。这是单独为每个板块，复制和渠道。可选可以进行数据转换，如log，Z-分数转型。
用法----------Usage----------
normalizePlates(x, normalizationMethod="median", transform, zscore, posControls, negControls, ...)
参数----------Arguments----------
参数：x
a cellHTS object that has already been configured. See details.
cellHTS已配置的对象。查看详情。
参数：normalizationMethod
a character specifying the normalization method to use for performing the per-plate normalization. Allowed values are "median" (default), "mean", "shorth", "POC", "NPI", "negatives" and Bscore. See details.
一个字符指定的规范化方法用于执行每板标准化。允许值"median"（默认），"mean"，"shorth"，"POC"，"NPI"，"negatives"和Bscore。查看详情。
参数：transform
a function that takes a numeric vector and returns a numeric vector of the same length; for example, the logarithm function log.
一个数值向量，函数返回一个相同长度的数字向量，例如，对数函数log。
参数：zscore
indicates if the data should be centered and scaled after normalization and transformation. If missing (default), the data will not be centered and scaled. Otherwise, the value of this argument should be a character string, either "+" or "-", which will be used to set the sign for the calculated z-scores. See details.
表明如果数据应为本，缩放后的标准化和改造。如果缺少（默认），数据不会被中心和缩放。否则，这个参数的值应该是一个字符串，无论是“+”或“ - ”，将用于计算Z-分数为标志。查看详情。
参数：posControls
a vector of regular expressions giving the name of the positive control(s). See details.
给予阳性对照（S）的名称的正则表达式的向量。查看详情。
参数：negControls
a vector of regular expressions giving the name of the negative control(s). See details.
给予的负面控制（S）的名称的正则表达式的向量。查看详情。
参数：...
Further arguments that get passed on to the function implementing the normalization method chosen by normalizationMethod. Currently, this is only used for Bscore.
进一步的参数被传递到功能实现标准化的方法normalizationMethod选择。目前，这仅仅是使用Bscore。
Details
详情----------Details----------
The normalization is performed in a plate-by-plate fashion.
归一盘一盘的时尚。
If normalizationMethod="median" (median scaling), plates effects are corrected by dividing each measurement by the median value across wells annotated as sample in x$wellAnno, for each plate and replicate.
如果normalizationMethod="median"（中位数缩放），板影响整个井的中值除以每个测量标注为纠正samplex$wellAnno，为每个板块和复制。
If normalizationMethod="mean" (mean scaling), the average in the sample wells is consider instead.
如果normalizationMethod="mean"（缩放），sample井是考虑，而不是平均。
If normalizationMethod="shorth" (scaling by the midpoint of the shorth), for each plate and replicate, the midpoint of the shorth of the distribution of values in the wells annotated as sample is calculated. Then, every measurement is divided by this value.
如果normalizationMethod="shorth"（结垢通过的shorth的中点）为每个板和复制，shorth值分布在井sample计算注明的中点。然后除以该值，每次测量。
If normalizationMethod="POC" (percent of control), for each plate and replicate, each measurement is divided by the average of the measurements on the plate positive controls, and multiplied by 100.
如果normalizationMethod="POC"（％控制），为每个板和复制，每个测量所测量的平均分为阳性对照盘子上，并乘以100。
If normalizationMethod="negatives" (scaling by the negative controls), for each plate and replicate, each measurement is divided by the median of the measurements on the plate negative controls.
如果normalizationMethod="negatives"（阴性对照缩放），每块板和复制，每个测量分为阴性对照盘子上测量的中位数。
If normalizationMethod="NPI" (normalized percent inhibition), each measurement is subtracted from the average of the intensities on the plate positive controls, and this result is divided by the difference between the means of the measurements on the positive and the negative controls.
如果normalizationMethod="NPI"（归一％抑制），每次测量中减去从平均强度板阳性对照，这一结果是积极的测量手段和阴性对照组之间的差异。
If normalizationMethod="Bscore" (B score), for each plate and replicate, the B score method is applied to remove plate effects and row and column biases. NOTE: if the argument 'transform' is given, the B score method is applied AFTER data transformation.
如果normalizationMethod="Bscore"（二分），每块板和复制，在B评分方法应用于去除板效应和行和列偏见。注意：如果参数的变换，给出了B的得分方法是数据转换后应用。
If transform is not missing, the chosen data transformation is applied. Most commonly, this option can be used to apply a log transformation.
transform如果不缺，选择数据转换应用。最常用的，这个选项可以用来申请log转换。
If zscore is not missing, a robust z-score for each individual measurement will be determined for each plate and each well by subtracting the overall median and dividing by the overall mad. These are taken by considering the distribution of intensities (over all plates) in the wells whose content is annotated as sample. The allowed values for zscore ("+" or "-") are used to set the sign of the calculated z-scores. For example, with a zscore="-" a strong decrease in the signal will be represented by a positive z-score, whereas setting zscore="+", such a phenotype will be represented by a negative z-score. This option can be set to calculate the results to the commonly used convention.
zscore如果不缺少，每个人测量一个强大的Z-分数将被确定为每块板，每口井减去整体median和除以整体mad。这些都被考虑的强度分布（超过所有板），其内容是sample注明的井。允许值zscore（“+”或“ - ”）是用于设置计算Z-分数的迹象。例如，zscore="-"在信号强的减少将代表积极Z-得分，而设置zscore="+"，这样的表型将负的Z-分数表示。此选项可以设置常用的“公约”的计算结果。
The arguments posControls and negControls are required for applying the normalization methods based on the control measurements (that is, when normalizationMethod="POC", or normalizationMethod="NPI", or normalizationMethod="negatives"). posControls and negControls should be given as a vector of regular expression patterns specifying the name of the positive(s) and negative(s) controls, respectivey, as provided in the plate configuration file (and stored in x$wellAnno). The length of these vectors should be equal to the number of reporters used in the screen (dim(x$xraw)[4]) or to dim(x$xnorm)[4], in case x contains multi-channel data that have been normalized by combining the values from two or more channels. By default, if posControls is not given, pos will be taken as the name for the wells containing positive controls. Similarly, if negControls is missing, by default neg will be considered as the name used to annotate the negative controls. The content of posControls and negControls will be passed to regexpr for pattern matching within the well annotation given in x$wellAnno (see examples for summarizeChannels). The arguments posControls and negControls are particularly useful in multi-channel data since the controls might be reporter-specific, or after normalizing multi-channel data.
的论点posControls和negControls都需要运用标准化的基础上控制测量方法（也就是说，当normalizationMethod="POC"或normalizationMethod="NPI"或normalizationMethod="negatives"） 。 posControls和negControls应作为向量的正则表达式指定模式（S）的积极和消极的（S）控制，respectivey板配置文件中提供的名称（和存储x$wellAnno）。这些向量的长度应该等于记者在屏幕上使用的数量（dim(x$xraw)[4]）dim(x$xnorm)[4]，x包含多通道数据相结合，已标准化从两个或多个通道的值。默认情况下，如果posControls没有给出，POS将视为包含阳性对照井的名称。同样，如果negControls缺少，默认情况下，NEG将被视为阴性对照用来注释的名称。 posControls和negControls将通过regexpr的在x$wellAnno给定的良好注释的模式匹配的内容（见summarizeChannels例子）。论据posControls和negControls是特别有用的，因为在多通道数据的控制可能是特定的记者，或标准化后多通道数据。
值----------Value----------
An object of class cellHTS, which is a copy of the argument x, plus an additional slot xnorm containing the normalized data. This is an array of the same dimensions as xraw.
cellHTS类的对象，这是一个参数的副本x，加上一个额外的插槽xnorm包含规范化的数据。这是一个xraw尺寸相同的数组。
Moreover, the processing status of the cellHTS object is updated in the slot state to x$state["normalized"]=TRUE.
此外，处理cellHTS对象的状态更新插槽statex$state["normalized"]=TRUE。
Additional outputs may be given if adjustPlates="Bscore". Please refer to the help page of the Bscore function.
如果adjustPlates="Bscore"可给予额外的产出。 Bscore函数，请参阅帮助页面。
作者（S）----------Author(s)----------
Ligia Braz <a href="mailto:ligia@ebi.ac.uk">ligia@ebi.ac.uk</a>, Wolfgang Huber
<a href="mailto:huber@ebi.ac.uk">huber@ebi.ac.uk</a>
参见----------See Also----------
Bscore, summarizeChannels
Bscore，summarizeChannels
举例----------Examples----------
data(KcViabSmall)
x1 = normalizePlates(KcViabSmall, normalizationMethod="median", zscore="-")
## Not run: [＃无法运行：]
x2 = normalizePlates(KcViabSmall, normalizationMethod="Bscore", zscore="-")
## End(Not run)[＃结束（不运行）]
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 14:21:25
