normalizeMethyLumiSet(methylumi)
normalizeMethyLumiSet()所属R语言包：methylumi
Normalize a MethyLumiSet, accounting for dye bias
规范化染料偏见MethyLumiSet的，会计
译者：生物统计家园网 机器人LoveR
描述----------Description----------
The Illumina GoldenGate methylation platform uses two colors, one to represent the unmethylated state and the other to represent the methylated state. This function corrects that dye bias and recalculates the betas based on the corrected intensities.
Illumina公司的GoldenGate甲基化平台使用两种颜色，代表的甲基化状态和其他代表的甲基化状态。此功能纠正，染料偏见和重新计算基于更正强度的“贝塔。
For HumanMethylation27 data, the function does nothing.
HumanMethylation27数据，函数什么都不做。
For HumanMethylation450 data, the function delegates to normalizeViaControls() the task of scaling red and green intensities against a reference array (chip) which defaults to the first chip in a set. The code to do this is based on code from the 'minfi' package and uses the built-in normalization controls to scale the channels of the samples, so that a consistent degree of dye bias is maintained for Infinium II probes across an experiment or set of experiments.
对于HumanMethylation450数据，默认为集合的第一个芯片的功能代表normalizeViaControls（）扩大对红色和绿色的强度参考阵列（芯片）的任务。做到这一点的代码基于从“minfi包的代码，并使用内置的标准化控制规模样品的渠道，染料偏见的一致程度，从而使维持整个实验或集Infinium二探针实验。
用法----------Usage----------
normalizeMethyLumiSet(x, beta.cuts = c(0.2, 0.8), mapfun = c("atan", "ratio"))
参数----------Arguments----------
参数：x
A MethyLumiSet object
一个MethyLumiSet对象
参数：beta.cuts
Two numeric values with the first less than the second and between 0 and 1, representing the beta cutoffs that will be used when determining the median intensities to which to correct. See details below.
两个第一比第二0和1之间的数值，代表的确定，中位数强度纠正时，将被用来测试截止。详见下文。
参数：mapfun
Either "atan" or "ratio". See details below.
无论是“ATAN”或“比”。详见下文。
Details
详情----------Details----------
For HumanMethylation450 data, the function delegates to normalizeViaControls() the task of scaling red and green intensities against a reference array (chip) which defaults to the first chip in a set. The code to do this is based on code from the 'minfi' package and uses the built-in normalization controls to scale the channels of the samples, so that a consistent degree of dye bias is maintained for Infinium II probes across an experiment or set of experiments. The remainder of the documentation below is specific to GoldenGate data.
对于HumanMethylation450数据，默认为集合的第一个芯片的功能代表normalizeViaControls（）扩大对红色和绿色的强度参考阵列（芯片）的任务。做到这一点的代码基于从“minfi包的代码，并使用内置的标准化控制规模样品的渠道，染料偏见的一致程度，从而使维持整个实验或集Infinium二探针实验。下面的文档的其余部分是具体的GoldenGate数据。
The Illumina GoldenGate methylation platform uses two colors, one to represent the unmethylated state and the other to represent the methylated state. This function corrects that dye bias and recalculates the betas based on the corrected intensities.
Illumina公司的GoldenGate甲基化平台使用两种颜色，代表的甲基化状态和其他代表的甲基化状态。此功能纠正，染料偏见和重新计算基于更正强度的“贝塔。
As a first step, the medians for each of Cy3 and Cy5 are calculated at high and low betas, representing the (nearly) fully methylated state and the (nearly) fully unmethylated states. Values of Cy3 and Cy5 that are negative are set to zero for this process. Then, the Cy5 medians are adjusted to match those of the Cy3 channel, thereby correcting the dye bias.
Cy3和Cy5的中位数，作为第一步，在高和低贝塔值计算，相当于（几乎）完全甲基化状态和完全甲基化（几乎）状态。 Cy3和Cy5为负的值设置为零，这个过程。然后，Cy5的中位数调整，以配合Cy3标记通道，从而纠正染料偏见。
To map the new intensities back to betas, one of two map functions can be used. The default is the atan(Cy3/Cy5). The ratio maps using the function (Cy3/Cy3+Cy5). The differences should be very small, but we feel that the atan map function is probably the mathematically appropriate way of doing this.
到新的强度映射到贝塔，两个映射功能可以使用。默认是ATAN（Cy3/Cy5）。比例图使用的功能（Cy3/Cy3 + Cy5标记）。差异应该是很小，但我们认为可能的的ATAN图功能是这样做的数学适当的方式。
值----------Value----------
A new "MethyLumiSet" that contains the corrected betas and the adjusted intensities.
一个新的“MethyLumiSet”，它包含校正贝塔和调整后的强度。
作者（S）----------Author(s)----------
Sean Davis <sdavis2@mail.nih.gov>
举例----------Examples----------
## Read in sample information[＃样品信息阅读]
samps <- read.table(system.file("extdata/samples.txt",
package = "methylumi"),sep="\t",header=TRUE)
## Perform the actual data reading[＃执行实际的数据读]
## This is an example of reading data from an [＃这是从一个读取数据的一个例子]
## Sentrix Array format file (actually two files,[的＃Sentrix阵列格式的文件（实际上是两个文件，]
## one for data and one for QC probes)[一个用于数据和质控探针）]
mldat <- methylumiR(system.file('extdata/exampledata.samples.txt',package='methylumi'),
qcfile=system.file('extdata/exampledata.controls.txt',package="methylumi"),
sampleDescriptions=samps)
mldatnorm <- normalizeMethyLumiSet(mldat)
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 2012-2-26 00:47:02
