dupcor(limma)
dupcor()所属R语言包：limma
Correlation Between Duplicates
之间重复的相关性
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Estimate the correlation between duplicate spots (regularly spaced replicate spots on the same array) or between technical replicates from a series of arrays.
估计重复点（定期间隔在同一阵列的复制点）之间的技术复制了一系列阵列之间的相关性。
用法----------Usage----------
duplicateCorrelation(object, design=rep(1,ncol(as.matrix(object))), ndups=2, spacing=1,
block=NULL, trim=0.15, weights=NULL)
参数----------Arguments----------
参数：object
a numeric matrix of expression values, or any data object from which as.matrix will extract a suitable matrix such as an MAList, marrayNorm or ExpressionSet object. If object is an MAList object then the arguments design, ndups, spacing and weights will be extracted from it if available and do not have to be specified as arguments. Specifying these arguments explicitly will over-rule any components found in the data object.
一个表达式的值的数字矩阵，或从as.matrix将提取如适合MAList，marrayNorm或ExpressionSet对象的矩阵，任何数据对象。 object如果是一个MAList对象，那么参数design，ndups，spacing和weights将提取（如果可用），它不必须被指定为参数。明确指定这些参数将超过排除在数据对象中发现的任何组件。
参数：design
the design matrix of the microarray experiment, with rows corresponding to arrays and columns to comparisons to be estimated. The number of rows must match the number of columns of object. Defaults to the unit vector meaning that the arrays are treated as replicates.
芯片实验设计矩阵，与估计的比较阵列和列对应的行。行数必须匹配object列数。默认的单位向量的含义，阵列被视为重复。
参数：ndups
a positive integer giving the number of times each gene is printed on an array. nrow(object) must be divisible by ndups. Will be ignored if block is specified.
给每一个基因的次数上印有一个正整数数组。 nrow(object)必须ndups整除的。如果block指定将被忽略。
参数：spacing
the spacing between the rows of object corresponding to duplicate spots, spacing=1 for consecutive spots
object相应的行之间的间距连续点的重复点，spacing=1
参数：block
vector or factor specifying a blocking variable
向量或指定阻塞变量的因素
参数：trim
the fraction of observations to be trimmed from each end of tanh(all.correlations) when computing the trimmed mean.
观测的一小部分被修剪从每个tanh(all.correlations)修剪平均计算。
参数：weights
an optional numeric matrix of the same dimension as object containing weights for each spot. If smaller than object then it will be filled out the same size.
一个可选的数字矩阵object包含每个点的权重相同的尺寸。如果不是object小然后将填写相同的大小。
Details
详情----------Details----------
When block=NULL, this function estimates the correlation between duplicate spots (regularly spaced within-array replicate spots). If block is not null, this function estimates the correlation between repeated observations on the blocking variable. Typically the blocks are biological replicates and the repeated observations are technical replicates. In either case, the correlation is estimated by fitting a mixed linear model by REML individually for each gene. The function also returns a consensus correlation, which is a robust average of the individual correlations, which can be used as input for functions lmFit or gls.series.
当block=NULL，这个功能估计的重复点（定期间距阵列内复制点）之间的相关性。 block如果不为空，这个功能估计重复观测上阻断变量之间的相关性。通常情况下，块是生物复制和重复观测技术复制。在任何情况下，单独拟合每一个基因的混合线性模型REML法估计相关。该函数也返回一个共识的相关性，这是一个强大的个人的相关性，可以作为输入功能lmFit或gls.series平均。
At this time it is not possible to estimate correlations between duplicate spots and between technical replicates simultaneously. If block is not null, then the function will set ndups=1, which is equivalent to ignoring duplicate spots.
在这个时候是无法估计的重复点和技术之间的复制，同时之间的相关性。 block如果不为空，则该函数将设置ndups=1，这是相当于忽略重复点。
For this function to return statistically useful results, there must be at least two more arrays than the number of coefficients to be estimated, i.e., two more than the column rank of design.
这个函数返回统计的有益成果，必须有至少两个以上系数的估计，即比列排名design两个阵列。
The function may take long time to execute as it fits a mixed linear model for each gene for an iterative algorithm. It is not uncommon for the function to return a small number of warning messages that correlation estimates cannot be computed for some individual genes. This is not a serious concern providing that there are only a few such warnings and the total number of genes is large. The consensus estimator computed by this function will not be materially affected by a small number of genes.
的功能可能需要很长一段时间来执行，因为它适合每一个基因的混合线性模型的一个迭代算法。它返回一个警告消息的少数相关估计不能用于计算一些单个基因的功能并不少见。这不是一个严重的问题，提供有只有几个这样的警告和基因总数是大。由这个函数计算的共识估计不会受到重大影响的基因少数。
值----------Value----------
A list with components
与组件列表
参数：consensus.correlation
the average estimated inter-duplicate correlation. The average is the trimmed mean of the individual correlations on the atanh-transformed scale.
平均估计重复间的相关性。平均是平均削减了个人ATANH转化的规模相关。
参数：cor
same as consensus.correlation, for compatibility with earlier versions of the software
consensus.correlation相同，该软件的早期版本的兼容性
参数：atanh.correlations
numeric vector of length nrow(object)/ndups giving the individual genewise atanh-transformed correlations.
长度的数字矢量nrow(object)/ndups给个人2-6。ATANH转化相关。
作者（S）----------Author(s)----------
Gordon Smyth
参考文献----------References----------
http://www.statsci.org/smyth/pubs/dupcor.pdf
参见----------See Also----------
These functions use mixedModel2Fit from the statmod package.
这些函数使用mixedModel2Fit，从statmod包的。
An overview of linear model functions in limma is given by 06.LinearModels.
线性模型功能概述limma由06.LinearModels给出。
举例----------Examples----------
# Also see lmFit examples[同时看lmFit例子]
## Not run: [＃无法运行：]
corfit <- duplicateCorrelation(MA, ndups=2, design)
all.correlations <- tanh(corfit$atanh.correlations)
boxplot(all.correlations)
fit <- lmFit(MA, design, ndups=2, correlation=corfit$consensus)
## End(Not run)[＃结束（不运行）]
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 23:14:08
