ArrayOutliers(arrayMvout)
ArrayOutliers()所属R语言包：arrayMvout
Multivariate outlier detection based on PCA of
基于PCA的多元异常检测
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Multivariate outlier detection based on PCA of
基于PCA的多元异常检测
用法----------Usage----------
ArrayOutliers (data, alpha, alphaSeq = c(0.01, 0.05, 0.1), ... )
# qcOutput = NULL, plmOutput = NULL, degOutput = NULL, prscale = TRUE,
# pc2use = 1:3)
参数----------Arguments----------
参数：data
an (affy) AffyBatch instance with at least 11 samples
至少有11个样本（affy的）AffyBatch实例
参数：alpha
false positive rate for outlier detection, adjusting for multiple comparisons according to Caroni and Prescott's adaptation of Rosner (1983); full report based on this choice of alpha
异常检测的误报率，多重比较的调整，根据卡罗尼和普雷斯科特的罗斯纳适应的（1983）;完整的报告基于这种选择的α
参数：alphaSeq
vector of alpha candidates to be quickly tried for short report
向量阿尔法候选人将迅速尝试简短的报告
参数：...
additional parameters, see below
额外的参数，见下文
Details
详情----------Details----------
Additional parameters may be supplied
可提供额外的参数
qcOutput optional result of simpleaffy qc() to speed computations
可选的结果simpleaffy QC qcOutput（），以加快计算
plmOutput optional result of affyPLM fitPLM() to speed computations
的affyPLM fitPLM（）plmOutput可选的结果，以加快计算
degOutput optional result of affy AffyRNAdeg() to speed computations
的affy AffyRNAdeg（）degOutput可选的结果，以加快计算
prscale scaling option for prcomp
prcomp prscale缩放选项
pc2use selection of principal components to use for outlier detection
pc2use主要部件的选择使用异常检测
Data elements afxsubDEG, afxsubQC, s12cDEG, s12cQC are precomputed RNA degradation and simpleaffy qc() results; s12c is an AffyBatch with digital contamination of some samples.
数据元素afxsubDEG，afxsubQC，s12cDEG，s12cQC预先计算的RNA降解和QC simpleaffy（）的结果; s12c是一个数字的一些样品污染AffyBatch。
Data elements maqcQA and itnQA are affymetrix QC statistics on large collections of arrays. Data element ilmQA is a derived from a LumiBatch of the Illumina-submitted MAQC raw data, 19 arrays. (Conveyed by Leming Shi, personal communication). Data element spikQA is a 12x9 matrix of QA parameters obtained for 12 arrays from U133A spikein dataset, with first 2 arrays digitally contaminated as described in Asare et al.
数据元素maqcQA和itnQA的是Affymetrix公司的QC统计阵列的大集合。数据的元素ilmQA是从Illumina公司提交MAQC原始数据，19阵列LumiBatch所得。 （乐明史，个人通信转达）。数据的元素spikQA是一个12x9矩阵，质量参数为12的U133A spikein集的阵列取得第2数字阵列在Asare等污染。
Data element fig3map gives the indices of the points labeled A-H in Figure 3 of the manuscript by Asare et al. associated with this package.
数据的元素fig3map给标记在图3的手稿由Asare等啊点的指数。与此包。
值----------Value----------
an instance of arrOutStruct class, a list with a partition of samples into two data frames (inl and outl) with QA summary statistics
例如，arrOutStruct类的样本分割成两个数据框与QA统计摘要（INL和OUTL）
作者（S）----------Author(s)----------
Z. Gao et al.
举例----------Examples----------
library(simpleaffy)
setQCEnvironment("hgu133acdf") # no CDF corresponding to tag array[民防部队没有相应的标记数组]
if ( require("mvoutData") ) {
data(s12c)
data(s12cQC)
data(s12cDEG)
library(affyPLM)
s12cPset = fitPLM(s12c)
ao = ArrayOutliers(s12c, alpha=0.05, qcOut=s12cQC, plmOut=s12cPset, degOut=s12cDEG)
ao
}
if (require("lumiBarnes")) {
library(lumiBarnes)
data(lumiBarnes)
ArrayOutliers(lumiBarnes, alpha=0.05)
lb2 = lumiBarnes
exprs(lb2)[1:20000,1:2] = 10000*exprs(lb2)[1:20000,1:2]
ArrayOutliers(lb2, alpha=0.05)
}
data(maqcQA) # affy[affy]
ArrayOutliers(maqcQA[,-c(1:2)], alpha=.05)
ArrayOutliers(maqcQA[,-c(1:2)], alpha=.01)
data(ilmQA) # illumina[Illumina公司]
ArrayOutliers(data.frame(ilmQA), alpha=.01)
data(itnQA) # 507 arrays from ITN[从蚊帐507阵列]
ArrayOutliers(itnQA, alpha=.01)
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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。
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发表于 2012-2-25 12:08:53
