norm.miR(ExiMiR)
norm.miR()所属R语言包：ExiMiR
miRNA raw data normalization function (low level)
miRNA的原始数据标准化功能（低电平）
译者：生物统计家园网 机器人LoveR
描述----------Description----------
A function which normalizes miRNA probe level intensities stored in an AffyBatch object. It uses the spike-in probe-based method by default. In case the spike-in probe-based method can not be applied, median normalization is executed instead. Several options allow to force the exectution of the spike-in probe-based normalization and to fine-tune the resulting correction functions.
规范化水平在AffyBatch对象中的miRNA探针强度函数。它使用默认情况下，穗探针为基础的方法。穗的情况下探针为基础的方法不能套用，中位数标准化执行。几个选项允许，迫使穗探针为基础的标准化exectution微调校正功能。
用法----------Usage----------
norm.miR( abatch,
method=c("spikein","mean","median"),
figures.show=TRUE,
figures.output=c("display","file"),
min.corr=0.5,
loess.span=-1,
extrap.points=2,
extrap.method=c("mean","linear"),
force.zero=FALSE,
cover.ext=0.5,
cover.int=1/3,
max.log2span=1,
verbose=TRUE)
参数----------Arguments----------
参数：abatch
An AffyBatch object.
一个AffyBatch对象。
参数：method
Character vector. By default, spikein method is used. mean or median can also be selected and are used in case the 'spike-in' method can not be applied.
特征向量。默认情况下，spikein方法。 mean或median也可以被选中，并使用情况下，“穗”的方法不能适用。
参数：figures.show
Logical. Default value is TRUE. Control figures are generated for the spikein method.
逻辑。默认值是TRUE。数字控制产生spikein方法。
参数：figures.output
Character vector. By default, display is used. Figures are shown to the screen. Using file generates the figures in PDF format in the working directory.
特征向量。默认情况下，display使用。数字显示在屏幕上。使用file在工作目录中的PDF格式生成的数字。
参数：min.corr
Numeric. Default value is 0.5. Minimal allowed value for the average of the off-diagonal elements of the Pearson correlation matrix of the spike-in probeset intensities across the arrays.
数字。默认值是0.5。关闭整个阵列穗在probeset强度的Pearson相关矩阵对角线元素的平均最小允许值。
参数：loess.span
Numeric. Default value is -1, which corresponds to a loess smoothing neighbourhood spanning a fraction 3/(number of spike-in probesets) of the total number of points. Other positive values are allowed, see the span argument of the R loess function
数字。默认值是-1，这相当于一个黄土平滑居委会跨越点总数的3 /（穗在probesets号）的一小部分。其他正面的价值观是允许的，看到的span的Rloess函数参数
参数：extrap.points
Numeric. Default value is 2. The number of spike-in probesets used in the high-intensity extrapolation of the normalization correction function.
数字。默认值是2。穗的数量在probesets用在高强度的标准化校正功能推断。
参数：extrap.method
Character vector. Default value is mean. The method used for the high-intensity extrapolation of the normalization correction function.
特征向量。默认值是mean。该方法用于标准化校正功能的高强度的推断。
参数：force.zero
Logical. Default value is FALSE. If TRUE, it forces the normalization correction functions to have zero values at the lower end of the probe intensity range.
逻辑。默认值是FALSE。如果TRUE，它迫使标准化校正功能，在探针强度范围的低端值为零。
参数：cover.ext
Numeric. Default value is 1/2. Minimal allowed relative coverage of the spike-in probesets intensities. It is computed as the ratio between the intensity range covered by the spike-in probes and the one covered by all probes on the array.
数字。默认值是1/2。最小允许相对覆盖的在穗probesets强度。据计算比之间的强度范围涵盖穗探针和一个阵列上的所有探针涵盖。
参数：cover.int
Numeric. Default value is 1/3. Maximal allowed relative intensity interval between two consecutive spike-in probesets. It is computed as the largest intensity difference between two consecutive spike-in probesets divided by the overall probe intensity range.
数字。默认值是1/3。最大允许连续两穗在probesets的相对强度间隔。据计算整体探针强度范围分为两个连续尖峰IN probesets最大的强度差。
参数：verbose
Logical. Default is TRUE; some details are provided on the console.
逻辑。默认TRUE;在控制台上提供的一些细节。
参数：max.log2span
Numeric. Default value is 1. Gives the maximal (log2) intensity interval allowed for the probes belonging to one spike-in probeset.
数字。默认值是1。给人最大的（log2）强度属于穗在probeset探针允许的时间间隔。
值----------Value----------
An AffyBatch object with expression data normalized.
AffyBatch对象表达数据的规范化。
作者（S）----------Author(s)----------
Sylvain.Gubian, Alain.Sewer, PMP SA
举例----------Examples----------
data(galenv)
data(GSE20122)
abatch.spike <- norm.miR(GSE20122)
# Apply the affy method hist on the generated AffyBatch object abatch.spike[申请的affy方法历史上生成AffyBatch对象abatch.spike]
layout(matrix(c(1,2), 1, 2, byrow = TRUE))
hist(GSE20122)
hist(abatch.spike)
layout(1)
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 17:17:37
