normalizeByReference(tilingArray)
normalizeByReference()所属R语言包：tilingArray
Probe-specific normalization of hybridization intensities from an oligonucleotide microarray
寡核苷酸芯片探针杂交强度标准化
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Adjust the hybridization intensities from an oligonucleotide microarray for probe-specific response effect by using one or several reference hybridizations. If x contains more than one array, vsnMatrix from the vsn package is called for between array normalization.
调整为寡核苷酸芯片探针的具体反应的影响，通过一个或几个参考杂交的杂交强度。如果x包含多个阵列，vsnMatrixvsn包称为数组标准化之间。
用法----------Usage----------
normalizeByReference(x, reference, pm, background, refSig, nrStrata=10,
cutoffQuantile=0.05, plotFileNames, verbose=FALSE)
参数----------Arguments----------
参数：x
ExpressionSet containing the data to be normalized.
ExpressionSet包含的数据进行标准化。
参数：reference
ExpressionSet with the same number of features as x, containing the reference signal, on the raw scale (non-logarithmic). This argument can be used to directly input the data from a set of replicate DNA hybridizations. Alternatively, the argument refSig can be specified.
与功能相同数量的ExpressionSetx，含有参考信号，对原材料的规模（非数）。此参数可用于直接输入数据，从一组的复制DNA的杂交。另外，参数refSig可以指定。
参数：pm
Indices specifying the perfect match features in reference (see Details). This can be either an integer vector with values between 1 and nrow(exprs(reference)) or a logical vector.
指定reference（见详情）的完美匹配功能的指数。这可以是一个值介于1和nrow(exprs(reference))或逻辑向量整数向量。
参数：background
Indices specifying a set of background features in x (see Details). This can be either an integer vector with values between 1 and nrow(exprs(x)) or a logical vector.
指定一组x（见详情）背景特征的指数。这可以是一个值介于1和nrow(exprs(x))或逻辑向量整数向量。
参数：refSig
A numeric vector of the same length as pm with estimates of probe response effects, on a logarithm-like scale. This argument can be specified alternatively to reference.
数字向量的长度相同pm探测响应的影响，在对数样的规模，估计。这种说法，可以指定或者reference。
参数：nrStrata
Integer (length 1), number of strata for the estimation of the background function.
整数（长度为1），地层为背景函数的估计数。
参数：cutoffQuantile
Numeric (length 1), the probes whose reference signal is below this quantile are thrown out.
数值（长度为1），下面是这个位数抛出的参考信号的探针。
参数：plotFileNames
Character vector whose length is the same as the number of arrays in x. Optional, if missing, no plots are produced.
特征向量，其长度为数组x的数量是相同的。可选的，如果丢失，无图生产。
参数：verbose
Logical of length 1, if TRUE, some messages about progress are printed.
长度为1，如果TRUE，对一些进展的消息打印逻辑。
Details
详情----------Details----------
The intensities in x are adjusted according to the reference values. Typically, the reference values are obtained by hybridizing a DNA sample to the array, so that the abundance of target is the same for all reference probes, and their signal can be used to estimate the probe sequence effect. A reference probe is a probe that perfectly matches the target genome exactly once. Usually, not all probes on a chip are reference probes, hence the subset of those that are is specified by the argument pm.
x强度根据参考值进行调整。通常情况下，获得杂交的DNA样本，以阵列的参考价值，丰富的目标是使所有参考探针相同，其信号可以用来估计探针序列的效果。参考探针是一个完全匹配一次目标基因组的探针。通常，并不是所有的在一个芯片上的探针参考探针，因此，这些是由参数pm指定的子集。
The background signal is estimated from the probes indicated by the argument background. They need to be a strict subset of the reference probes. I.e., they need to uniquely match the target organism's DNA, but are not expected to match any of its transcripts. A robust estimation method is used, so a small fraction of background probes that do hit transcripts is not harmful.
估计从参数background表示探针的背景信号。他们需要的是严格的reference探针子集。也就是说，他们需要的唯一目标生物体的DNA相匹配，但预计不会匹配任何成绩单。一种稳健估计方法，所以不会对人体有害的background探针，不打成绩单的一小部分。
A limitation of this normalization method is that it only makes sense for the data from reference probes, NA values are returned for all other probes.
一本归一化方法的局限性在于，它不仅使参考探针的数据意识，不适用的值是所有其他探测器传回。
The functions PMindex and BGindex can be used to produce the pm and background arguments from a probeAnno environment such as provided in the davidTiling package.
职能PMindex和BGindex可以用来生产pm和background参数从probeAnno如在davidTiling包的环境。
To summarize, a reference probe (indicated by argument pm) is a probe that perfectly matches the target genome exactly once, a background probe (indicated by argument background) is a reference probe which we expect not to be transcribed. These should not be confused with what is called 'perfect match' and 'mismatch' probes in Affymetrix annotation.
总结，参考探针（参数表示pm）是完全匹配一次目标基因组的探针，背景探测器（参数表示background），我们不希望是一个参考探针被转录。这些不应该被混淆，什么叫做“珠联璧合”，“错配”Affymetrix的注释探针。
值----------Value----------
A copy of x with the normalized intensities.
一个x归强度的副本。
作者（S）----------Author(s)----------
W. Huber <a href="mailto:huber@ebi.ac.uk">huber@ebi.ac.uk</a>
参考文献----------References----------
参见----------See Also----------
PMindex, BGindex
PMindex，BGindex
举例----------Examples----------
## see vignette assessNorm.Rnw in inst/scripts directory[＃INST / scripts目录中的小插曲assessNorm.Rnw]
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。
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发表于 2012-2-26 15:34:38
