normaliseIllumina(beadarray)
normaliseIllumina()所属R语言包：beadarray
Normalise Illumina expression data
Normalise Illumina的表达数据
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Normalises expression intensities from an ExpressionSetIllumina object so that the intensities are comparable between arrays.
NormalisesExpressionSetIllumina对象，这样的强度是可比阵列之间的表达强度。
用法----------Usage----------
normaliseIllumina(BSData, method="quantile", transform="none", T=NULL, status=fData(BSData)$Status,negctrl="negative",regular="regular",...)
参数----------Arguments----------
参数：BSData
an ExpressionSetIllumina object
ExpressionSetIllumina对象
参数：method
character string specifying normalisation method (options are "quantile", "qspline", "vsn", "rankInvariant", "median" and "none".
字符串指定标准化的方法（选项"quantile""qspline"，"vsn"，"rankInvariant"，"median"和"none"。
参数：transform
character string specifying transformation to apply to the data prior to normalisation (options are "none", "log2", neqc, rsn and "vst"
字符串指定的改造，适用于数据（选项"none"，"log2"，neqc，rsn和"vst"标准化之前
参数：T
A target distribution vector used when method="rankInvariant" normalisation. If NULL, the mean is used.
一个目标分配的向量，用时method="rankInvariant"标准化。如果NULL，平均使用的。
参数：status
character vector giving probe types (used in neqc normalisation only)
特征向量，探针类型（用于仅在neqc标准化）
参数：negctrl
character vector giving negative control probes (used in neqc normalisation only)
特征向量，阴性对照探针（用于仅在neqc标准化）
参数：regular
character vector giving regular probes (used in neqc normalisation only)
特征向量，定期探针（仅在neqc标准化）
参数：...
further arguments to be passed to lumiT or neqc
进一步的参数被传递给lumiT或neqc
Details
详情----------Details----------
Normalisation is intended to remove from the expression measures any systematic trends which arise from the microarray technology rather than from differences between the probes or between the target RNA samples hybridized to the arrays.
标准化的目的是从表达中删除的任何措施，从芯片技术，而不是从之间的探针杂交阵列的靶RNA样品之间的差异或出现系统性的趋势。
In this function, the transform specified by the user is applied prior to the chosen normalisation procedure.
在这个函数中，transform由用户指定的应用之前所选择的标准化过程。
When transform="vst" the variance-stabilising transformation from the 'lumi' package is applied to the data. Refer to the lumiT documentation for further particulars. Note that the Detection P values are only passed on when they are available (i.e. not NA). The rsn option calls code directly from lumi.
当transform="vst"从“LUMI”包方差稳定的转化应用的数据。参考lumiT进一步详情的文件。请注意，只有通过检测P值可用时（即不适用）。 RSN选项调用代码直接从lumi。
For further particulars on the different normalisation methods options refer to the individual help pages (?normalize.quantiles for "quantile", ?normalize.qspline for "qspline", ?rankInvariantNormalise for "rankInvariant", ?medianNormalise for "median" and ?vsn2 for "vsn".
对于不同的标准化方法选项的进一步详情请参阅个别帮助页（?normalize.quantiles"quantile"，?normalize.qspline的“qspline”，?rankInvariantNormalise"rankInvariant" ?medianNormalise"median"和?vsn2"vsn"。
For median normalisation, the intensity for each gene is adjusted by subtracting the median of all genes on the array and then adding the median across all arrays. The effect is that each array then has the same median value.
中位数的标准化，为每一个基因的强度减去阵列上的所有基因的中位数，然后加入所有阵列中位数调整。效果，然后每个阵列具有相同的中值。
Note: If your BSData object contains data already on the log-scale, be careful that you choose an appropriate transform to avoid transforming it twice. The same applies for the "vst" transformation and "vsn" normalisation methods which require the expression data stored in BSData to be on the original (un-logged) scale. When method="vsn", transform must be set to "none", since this method transforms and normalises the data as part of the model.
注：如果你的BSData对象包含的数据已经在log规模，要小心，你选择一个合适的transform避免两次转化。同样适用于改造和"vst"标准化的方法，需要表达数据存储在"vsn" BSData是在原始（未记录）的规模。当method="vsn"，变换必须设置为"none"，因为这种方法的转变和normalises数据作为模型的一部分。
The neqc normalisation is described in Shi et al (2010) and documented in the limma package. Note that the output from this method has control probes removed.
在石等人（2010）描述neqc标准化和记录在limma包。请注意，这种方法的输出控制探针删除。
值----------Value----------
An 'ExpressionSetIllumina' object which conatains the transformed and normalised expression values for each array.
一个“ExpressionSetIllumina”的对象conatains为每个阵列的转化和规范化的表达值。
作者（S）----------Author(s)----------
Matt Ritchie and Mark Dunning
参考文献----------References----------
举例----------Examples----------
if(require(beadarrayExampleData)){
data(exampleSummaryData)
exampleSummaryData.norm = normaliseIllumina(channel(exampleSummaryData, "G"), method="quantile", transform="none")
exampleSummaryData.rsn = normaliseIllumina(channel(exampleSummaryData, "G.ul"),method="rsn", transform="none")
}
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 2012-2-25 12:43:58
