normalizeChannels(cellHTS)
normalizeChannels()所属R语言包：cellHTS
Normalization of dual-channel data and data transformation
双通道数据的规范化和数据转换
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Normalizes and/or transforms dual-channel data xraw of a given cellHTS object by applying the function defined in fun. The default is to take the ratio between the second and first channels (r2/r1). Correction of plate-to-plate variations may also be performed.
标准化和/或转换双通道的数据xraw一个给定的cellHTS应用fun定义的函数的对象。默认是采取第二和第一通道（r2/r1）之间的比率。也可以进行矫正板对板的变化。
用法----------Usage----------
normalizeChannels(x, fun = function(r1,r2) r2/r1, log = FALSE,
adjustPlates, zscore, posControls, negControls, ...)
参数----------Arguments----------
参数：x
a cellHTS object that has already been configured. See details.
1 cellHTS对象已配置。查看详情。
参数：fun
a function defined by the user to relate the signal in the two channels r1 and r2. fun takes two numeric vectors and returns a numeric vector of the same length. The default is to take the ratio between the second and first channels.
由用户定义的函数涉及的信号在两个通道r1和r2。 fun需要两个数值向量，并返回一个同样长度的数字向量。默认是第二和第一通道之间的比例。
参数：log
a logical value indicating whether the result obtained after applying fun should be log2 transformed. The default is log = FALSE, and the data is not log2 transformed.
一个逻辑值，指明是否申请fun应该是log2转化后得到的结果。默认是log = FALSE，数据是不log2转化。
参数：adjustPlates
character string indicating the correction method to apply to adjust for plate-to-plate variations (and eventually well-to-well variations), after applying fun and eventually log transforming the values. Allowed values are "median", "mean", "shorth", "POC", "NPI", "negatives" and Bscore. If adjustPlates is missing (the default), no plate-wise correction will be performed. See details.
字符串，指示板到板的变化（最终富裕的良好变化），适用于调整后申请fun并最终记录转化值的校正方法。允许的值是"median"，"mean"，"shorth"，"POC"，"NPI"，"negatives"和Bscore。如果adjustPlates丢失（默认），将执行无板明智的校正。查看详情。
参数：zscore
indicates if the z-scores should be determined after normalization and transformation. If missing (default), the data will not be scored. Otherwise, it should be a character string, either "+" or "-", specifying the sign to use for the calculated z-scores. See details.
表示，如果Z-分数应标准化和改造后确定。如果失踪（默认），数据不会被拿下。否则，它应该是一个字符串，无论是“+”或“ - ”，指定用于计算Z-分数的迹象。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 adjustPlates. 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adjustPlates选择。目前，这仅仅是使用Bscore。
Details
详情----------Details----------
For each plate and replicate of a two-color experiment, the function defined in fun is applied to relate the intensity values in the two channels of the cellHTS object. The default is to calculate the ratio between the second and the first channels, but other options can be defined.
对于每块板和两色的实验复制，fun定义的功能适用于涉及在cellHTS对象的两个通道的强度值。默认是第二和第一渠道之间的比例计算，但可以定义其他选项。
If log = TRUE, the data obtained after applying fun is log2 transformed. The default is log = FALSE.
如果log = TRUE，申请fun是log2转化后得到的数据。默认log = FALSE。
If adjustPlates is not missing, the obtained values will be further corrected for plate effects by considering the chosen normalization method. The available options are:
如果adjustPlates不缺，得到的值将进一步纠正板的影响，考虑选择的归一化法。可用的选项是：
If adjustPlates="median" (median scaling), plates effects are corrected by dividing each measurement by the median value across wells annotated as sample in x$wellAnno, for each plate and replicate. If the data values are in log2 scale (log=TRUE), the per-plate factor is subtracted from each measurement, instead.
如果adjustPlates="median"（中位数缩放），板影响整个井的中值除以每个测量标注为纠正samplex$wellAnno，为每个板块和复制。如果数据值是在log2规模（log=TRUE），每盘的因素中减去从每个测量，而不是。
If adjustPlates="mean" (mean scaling), the average in the sample wells is consider instead. If the data values are in log2 scale (log=TRUE), the per-plate factor is subtracted from each measurement, instead.
如果adjustPlates="mean"（缩放），sample井是考虑，而不是平均。如果数据值是在log2规模（log=TRUE），每盘的因素中减去从每个测量，而不是。
If adjustPlates="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 (if log=FALSE) or subtracted by it (if log=TRUE, meaning that data have been log transformed).
如果adjustPlates="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，每个测量这个值除以（如果log=FALSE）或它减去（如果log=TRUE，这意味着数据已经log转换）。
If adjustPlates="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 multipliplied by 100.
如果adjustPlates="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，由100 multipliplied。
If adjustPlates="negatives", for each plate and replicate, each measurement is divided by the median of the measurements on the plate negative controls. If the data values are in log2 scale (log=TRUE), the per-plate factor is subtracted from each measurement, instead.
如果adjustPlates="negatives"，为每个板块和复制，每个测量除以阴性对照盘子上的测量中位数。如果数据值是在log2规模（log=TRUE），每盘的因素中减去从每个测量，而不是。
If adjustPlates="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adjustPlates="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 adjustPlates="Bscore" (Bscore), for each plate and replicate, the B score method is applied to remove plate effects and row and column biases.
如果adjustPlates="Bscore"（Bscore），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。
By default, adjustPlates is missing.
默认情况下，adjustPlates丢失。
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. The overall median and mad 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，每口井减去整体中位数除以整体狂。整体中位数和疯狂是被考虑的强度分布（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/or negControls are required for applying the normalization methods based on the control measurements (that is, when adjustPlates="POC", or adjustPlates="NPI" or adjustPlates="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$wellAnno). The length of these vectors should be equal to the final number of reporters, which in this case is always one. By default, if posControls is not given, "pos" will be taken as the name for the wells containing positive controls. Similarly, if negControls is missing, by default "neg" will be considered as the name used to annotate the negative controls. The content of posControls and negControls will be passed to regexpr for pattern matching within the well annotation given in x$wellAnno (see examples). 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.
论据posControls和/或negControls申请标准化的基础控制测量（也就是说，当adjustPlates="POC"或adjustPlates="NPI"或adjustPlates="negatives"方法 ）。 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$wellAnno）。这些向量的长度应该等于最后的数字，在这种情况下，始终是一个记者。默认情况下，如果posControls没有给出，“POS”将被视为包含阳性对照井的名字。同样，如果negControls缺少，默认情况下，“南德”将被视为阴性对照用来注释的名称。 posControls和negControls将传递给regexpr在x$wellAnno（见例子）给出了很好的注释模式匹配的内容。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, except in the dimension corresponding to the number of channels, since the two-channel intensities have been combined into one intensity value.
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。这是数组xraw，除了在尺寸相应的通道数量，因为双通道强度已合并成一个强度值相同的尺寸。
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----------
normalizePlates, summarizeChannels, Bscore,
normalizePlates，summarizeChannels，Bscore
举例----------Examples----------
## Not run: [＃无法运行：]
datadir <- system.file("DualChannelScreen", package = "cellHTS")
x <- readPlateData("Platelist.txt", "TwoColorData", path=datadir)
x <- configure(x, "Plateconf.txt", "Screenlog.txt", "Description.txt", path=datadir)
table(x$wellAnno)
## Define the controls for the different channels:[＃定义为不同的渠道控制：]
negControls=vector("character", length=dim(x$xraw)[4])
## channel 1 - gene A[1＃通道 - 一个基因]
## case-insensitive and match the empty string at the beginning and end of a line (to distinguish between "geneA" and "geneAB", for example, although this is not a problem for the well annotation in this example)[＃不区分大小写，匹配空字符串的开始和结束行（区分“geneA”和“geneAB”，例如，虽然这不是一个问题，在这个例子很好注释）]
negControls[1]= "(?i)^geneA$"
## channel 2 - gene A and geneB[2＃通道 - 基因A和geneB]
negControls[2]= "(?i)^geneA$|^geneB$"
posControls = vector("character", length=dim(x$xraw)[4])
## channel 1 - no controls[1＃通道 - 无控制]
## channel 2 - geneC and geneD[＃2通道 - geneC和geneD]
posControls[2]="(?i)^geneC$|^geneD$"
writeReport(x, posControls=posControls, negControls=negControls)
x = normalizeChannels(x, fun=function(x,y) y/x, log=TRUE, adjustPlates="median")
## Define the controls for the normalized intensities (only one channel):[定义归强度（只有一个通道）的控制：]
negControls = vector("character", length=dim(x$xnorm)[4])
## For the single channel, the negative controls are geneA and geneB [＃对于单通道，阴性对照的是geneA和geneB]
negControls[1]= "(?i)^geneA$|^geneB$"
posControls = vector("character", length=dim(x$xnorm)[4])
## For the single channel, the negative controls are geneC and geneD [＃对于单个通道阴性对照geneC的和geneD]
posControls[1]="(?i)^geneC$|^geneD$"
writeReport(x, force=TRUE, plotPlateArgs=list(xrange=c(-3,3)),
posControls=posControls, negControls=negControls)
## 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 14:21:17
