nudge1(nudge)
nudge1()所属R语言包：nudge
Function for normalizing data, fitting a normal-uniform mixture and estimating probabilities of differential expression in the case where the two samples are being compared directly
功能标准化数据，拟合一个正常的均匀混合物，估计的情况下差异表达的概率，其中两个样本被直接比较
译者：生物统计家园网 机器人LoveR
描述----------Description----------
After a mean and variance normalization, a two component mixture model is fitted to the data. The normal component represents the genes that are not differentially expressed and the uniform component represents the genes that are differentially expressed. Posterior probabilities for differential expression are computed from the fitted model.
均值和方差标准化后，两个组件的混合模型拟合数据。正常的部分代表是没有差异表达和统一组件代表的差异表达基因的基因。差异表达的后验概率计算的拟合模型。
用法----------Usage----------
nudge1(logratio, logintensity, dye.swap = FALSE, span1 = 0.6, span2 = 0.2,
quant = 0.99, z = NULL, tol = 0.00001,iterlim=500)
参数----------Arguments----------
参数：logratio
A matrix or vector of log (base 2) ratios of intensity expressions in 2 samples, with rows indexing genes and columns (if necessary) indexing replicates.
log矩阵或矢量（碱基）的比率在2个样品的强度表达，行索引基因和索引重复的列（如有必要）。
参数：logintensity
A matrix or vector of total log (base 2) total intensities (defined as the product) of intensity expressions in 2 samples, with rows indexing genes and columns (if necessary) indexing replicates.
总记录矩阵或向量（碱基）的总强度（定义为产品），2个样品的强度表达式索引复制的行的索引基因和列（如有必要）。
参数：dye.swap
A logical value indicating whether or not the data is from a balanced dye-swap. Only used for multiple replicate experiments.
一个逻辑值，该值指示数据是否是从均衡染料交换。仅用于多个重复实验。
参数：span1
Proportion of data used to fit the loess regression of the (average-across-replicates) log ratios on the (average-across-replicates) log total intensities for the mean normalization.
使用适合的黄土上（平均对面的复制）（平均对面，复制）log比率回归的数据记录平均标准化的总强度的比例。
参数：span2
Proportion of data used to fit the loess regression of the absolute (mean normalized) log ratios on the log total intensities for the variance normalization. Only used for single replicate experiments.
适合局部加权回归的绝对（平均归）loglog上方差标准化的总强度比使用数据的比例。仅用于单一的重复实验。
参数：quant
Quantile to be used from the distribution of standard deviations of log ratios across replicates for all genes whose standard deviation was smaller than their absolute (mean normalized) average-across-replicates log ratio. Only used for multiple replicate experiments.
位数将用于从分布的标准偏差的log比跨所有的基因，其标准差小于其绝对复制（平均归一化）平均全面复制log的比例。仅用于多个重复实验。
参数：z
An optional 2-column matrix with each row giving a starting estimate for the probability of the gene (in the corresponding row of the log ratio matrix/vector) not being differentially expressed and a starting estimate for the probability of the gene being differentially expressed. Each row should add up to 1.
可选2列矩阵每行一个基因的概率估计（在相应的行数比矩阵/矢量）没有差异表达基因的概率为估计差异表达。每一行加起来应该为1。
参数：tol
A scalar tolerance for relative convergence of the loglikelihood.
一个标量相对收敛的loglikelihood宽容。
参数：iterlim
The maximum number of iterations the EM is run for.
最大迭代次数的EM运行。
Details
详情----------Details----------
A balanced dye swap is where a certain number of replicates have a particular dye to sample assigment and the same number of other replicates have the reversed assignment. Note in this case log ratios should be taken with numerators being the same sample and denominators the other sample, i.e. ratios should always be sample i/sample j rather than red dye/green dye for all replicates.
一个平衡的染料交换一定数量的复制有一个特别的染料来的样品assigment和相同数量的其他复制有扭转分配。注意在这种情况下，log比率应采取同一样品的分子和分母的其他样本，即比率应始终是样品I /样本j，而不是红色染料/所有复制的绿色染料。
值----------Value----------
A list including the following components
包括以下组件的列表
参数：pdiff
A vector with the estimated posterior probabilities of being in the group of differentially expressed genes.
与中差异表达的基因组后验概率估计的向量。
参数：lRnorm
A vector with the normalized (average-across-replicates) log ratios.
归（平均全面复制）log比率向量。
参数：mu
The estimated mean of the group of genes that are not differentially expressed.
估计是没有差异表达的基因组平均。
参数：sigma
The estimated variance of the group of genes that are not differentially expressed.
估计是没有差异表达的基因组变异。
参数：mixprob
The prior/mixing probability of a gene being in the group of genes that are not differentially expressed.
一个没有差异表达的基因组中基因的前/混合概率。
参数：a
The minimum value of the normalized data.
规范化数据的最低值。
参数：b
The maximum value of the normalized data.
规范化数据的最大价值。
参数：loglike
The log likelihood for the fitted mixture model.
拟合混合模型的log的可能性。
参数：iter
The number of iterations run by the EM algorithm until either convergence or iteration limit was reached.
EM算法的运行，直到达到收敛或迭代限制的迭代的数量。
作者（S）----------Author(s)----------
N. Dean and A. E. Raftery
参考文献----------References----------
参见----------See Also----------
nudge2,norm1a,norm1b,norm1c,norm1d,norm2c,norm2d
nudge2，norm1a，norm1b，norm1c，norm1d，norm2c，norm2d
举例----------Examples----------
data(like)
lR<-log(like[,1],2)-log(like[,2],2)
lI<-log(like[,1],2)+log(like[,2],2)
result<-nudge1(lR,lI)
data(hiv)
lR<-log(hiv[,1:4],2)-log(hiv[,5:8],2)
lI<-log(hiv[,1:4],2)+log(hiv[,5:8],2)
result<-nudge1(lR,lI,dye.swap=TRUE)
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 2012-2-26 07:57:29
