R语言 marray包 marrayNorm-class()函数中文帮助文档(中英文对照)

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marrayNorm-class(marray)
marrayNorm-class()所属R语言包：marray

                                        Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data
                                         类“marrayNorm”，类和标准化后的cDNA微阵列强度数据的方法

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

This class represents post-normalization intensity data for a batch of cDNA microarrays. A batch of arrays consists of a collection of arrays with the same layout  ("marrayLayout"). The class contains slots for the average log-intensities A, the normalized log-ratios M, the location and scale normalization values, the layout of the arrays, and descriptions of the target samples hybridized to the arrays and probe sequences spotted onto the arrays.
这个类代表的一批基因芯片标准化后的强度数据。一批阵列组成具有相同的布局（"marrayLayout"）数组的集合。类包含插槽的平均log强度，归log比男，地点和规模的标准化值，阵列的布局，杂交到阵列发现的阵列和探针序列的目标样本的描述。


类的对象----------Objects from the Class----------

Objects can be created by calls of the form    new('marrayNorm',<br>     maA        = ...., # Object of class matrix<br>     maM        = ...., # Object of class matrix<br>     maMloc     = ...., # Object of class matrix<br>     maMscale   = ...., # Object of class matrix<br>     maW        = ...., # Object of class matrix<br>     maLayout   = ...., # Object of class marrayLayout<br>     maGnames   = ...., # Object of class marrayInfo<br>     maTargets  = ...., # Object of class marrayInfo<br>     maNotes    = ...., # Object of class character<br>     maNormCall = ...., # Object of class call<br>   )
可以创建对象调用的形式  new('marrayNorm',参考    maA        = ...., # Object of class matrix参考    maM        = ...., # Object of class matrix参考    maMloc     = ...., # Object of class matrix参考    maMscale   = ...., # Object of class matrix参考     maW        = ...., # Object of class matrix参考    maLayout   = ...., # Object of class marrayLayout参考    maGnames   = ...., # Object of class marrayInfo参考    maTargets  = ...., # Object of class marrayInfo参考    maNotes    = ...., # Object of class character参考    maNormCall = ...., # Object of class call参考<X >


插槽----------Slots----------




maA: Object of class "matrix", average log-intensities (base 2) A, rows correspond to spotted probe sequences, columns to arrays in the batch.
maA类"matrix"，平均log强度（基数为2），行斑点探针序列，批次中的数组的列对应的对象。




maM: Object of class "matrix", intensity log-ratios (base 2) M, rows correspond to spotted probe sequences, columns to arrays in the batch.
maM：Object类的"matrix"，强度log比率（基数为2）男，行对应的斑点探针序列，列在批次阵列。




maMloc: Object of class "matrix", location normalization values, rows correspond to spotted probe sequences, columns to arrays in the batch.
maMloc：类"matrix"，位置标准化值的对象，行对应的斑点探针序列，列在批次阵列。




maMscale: Object of class "matrix",  scale normalization values, rows correspond to spotted probe sequences, columns to arrays in the batch.
maMscale：类"matrix"，规模标准化值的对象，行对应的斑点探针序列，列在批次阵列。




maW: Object of class "matrix", spot quality weights, rows correspond to spotted probe sequences, columns to arrays in the batch.
maW："matrix"，现场质量权重类，行对应斑点探针序列，列在批次阵列物件。




maLayout: Object of class "marrayLayout", layout parameters for cDNA microarrays.
maLayout类"marrayLayout"，cDNA微阵列布局参数的对象。




maGnames: Object of class "marrayInfo", description of spotted probe sequences.
maGnames类"marrayInfo"，斑点探针序列描述的对象。




maTargets: Object of class "marrayInfo", description of target samples hybridized to the arrays.
maTargets类"marrayInfo"，杂交阵列的目标样本的描述对象。




maNotes: Object of class "character", any notes concerning the microarray experiments, e.g. hybridization or scanning conditions.
maNotes：Object类的"character"，任何关于微阵列实验的笔记，例如：杂交或扫描条件。




maNormCall: Object of class "call", function call for normalizing the batch of arrays.
maNormCall类"call"，标准化一批阵列函数调用的对象。


方法----------Methods----------




[ signature(x = "marrayNorm"):  subsetting operator for spots on the array and arrays in the batch, ensures that all slots are subset properly.
[signature(x = "marrayNorm")：批次中的阵列和阵列子集点的经营者，确保所有槽正确的子集。




coerce signature(from = "marrayRaw", to = "marrayNorm"): coerce an object of class "marrayRaw" into an object of class marrayNorm.
要挟signature(from = "marrayRaw", to = "marrayNorm")：强制类的对象"marrayRaw"类marrayNorm的对象。




maA signature(object = "marrayNorm"): slot accessor method.
MAAsignature(object = "marrayNorm")：插槽存取的方法。




maA<- signature(object = "marrayNorm", value = "matrix"): slot assignment method.
MAA < - signature(object = "marrayNorm", value = "matrix")：时隙分配方法。




maControls<- signature(object = "marrayNorm"): slot assignment method.
maControls < - signature(object = "marrayNorm")：时隙分配方法。




maControls signature(object = "marrayNorm"): slot accessor method.
maControlssignature(object = "marrayNorm")：插槽存取方法。




maGnames signature(object = "marrayNorm"): slot accessor method.
maGnamessignature(object = "marrayNorm")：插槽存取方法。




maGnames<- signature(object = "marrayNorm", value = "marrayInfo"): slot assignment method.
maGnames < - signature(object = "marrayNorm", value = "marrayInfo")：时隙分配方法。




maGridCol signature(object = "marrayNorm"): method which computes a vector of grid column coordinates for each spot.
maGridColsignature(object = "marrayNorm")：计算网格的列向量的方法为每个点的坐标。




maGridRow signature(object = "marrayNorm"): method which computes a vector of grid row coordinates for each spot.
maGridRowsignature(object = "marrayNorm")：计算网格行向量的方法为每个点的坐标。




maLayout signature(object = "marrayNorm"): slot accessor method.
maLayoutsignature(object = "marrayNorm")：插槽存取方法。




maLayout<- signature(object = "marrayNorm", value = "marrayLayout"): slot assignment method.
maLayout < - signature(object = "marrayNorm", value = "marrayLayout")：时隙分配方法。




maM signature(object = "marrayNorm"): slot accessor method.
MAMsignature(object = "marrayNorm")：插槽存取方法。




maM<- signature(object = "marrayNorm", value = "matrix"): slot assignment method.
MAM < - signature(object = "marrayNorm", value = "matrix")：时隙分配方法。




maMloc signature(object = "marrayNorm"): slot accessor method.
maMlocsignature(object = "marrayNorm")：插槽存取方法。




maMloc<- signature(object = "marrayNorm", value = "matrix"): slot assignment method.
maMloc < - signature(object = "marrayNorm", value = "matrix")：时隙分配方法。




maMscale signature(object = "marrayNorm"): slot accessor method.
maMscalesignature(object = "marrayNorm")：插槽存取方法。




maMscale<- signature(object = "marrayNorm", value = "matrix"): slot assignment method.
maMscale < - signature(object = "marrayNorm", value = "matrix")：时隙分配方法。




maNgc signature(object = "marrayNorm"): slot accessor method.
maNgcsignature(object = "marrayNorm")：插槽存取方法。




maNgc<- signature(object = "marrayNorm", value = "numeric"): slot assignment method.
maNgc < - signature(object = "marrayNorm", value = "numeric")：时隙分配方法。




maNgr signature(object = "marrayNorm"): slot accessor method.
maNgrsignature(object = "marrayNorm")：插槽存取方法。




maNgr<- signature(object = "marrayNorm", value = "numeric"): slot assignment method.
maNgr < - signature(object = "marrayNorm", value = "numeric")：时隙分配方法。




maNormCall signature(object = "marrayNorm"): slot accessor method.
maNormCallsignature(object = "marrayNorm")：插槽存取方法。




maNotes signature(object = "marrayNorm"): slot accessor method.
maNotessignature(object = "marrayNorm")：插槽存取方法。




maNotes<- signature(object = "marrayNorm", value = "character"): slot assignment method.
maNotes < - signature(object = "marrayNorm", value = "character")：时隙分配方法。




maNsamples signature(object = "marrayNorm"): slot accessor method.
maNsamplessignature(object = "marrayNorm")：插槽存取方法。




maNsc signature(object = "marrayNorm"): slot accessor method.
maNscsignature(object = "marrayNorm")：插槽存取方法。




maNsc<- signature(object = "marrayNorm", value = "numeric"): slot assignment method.
maNsc < - signature(object = "marrayNorm", value = "numeric")：时隙分配方法。




maNspots signature(object = "marrayNorm"): slot accessor method.
maNspotssignature(object = "marrayNorm")：插槽存取方法。




maNspots<- signature(object = "marrayNorm", value = "numeric"): slot assignment method.
maNspots < - signature(object = "marrayNorm", value = "numeric")：时隙分配方法。




maNsr signature(object = "marrayNorm"): slot accessor method.
maNsrsignature(object = "marrayNorm")：插槽存取方法。




maNsr<- signature(object = "marrayNorm", value = "numeric"): slot assignment method.
maNsr < - signature(object = "marrayNorm", value = "numeric")：时隙分配方法。




maPlate signature(object = "marrayNorm"): slot accessor method.
maPlatesignature(object = "marrayNorm")：插槽存取方法。




maPlate<- signature(object = "marrayNorm"): slot assignment method.
maPlate < - signature(object = "marrayNorm")：时隙分配方法。




maPrintTip signature(object = "marrayNorm"): method which computes a vector of print-tip-group indices for each spot.
maPrintTipsignature(object = "marrayNorm")：计算每个点的打印头组指数向量的方法。




maSpotCol signature(object = "marrayNorm"): method which computes a vector of spot column coordinates for each spot.
maSpotColsignature(object = "marrayNorm")：计算一个现货列向量的方法，为每个点的坐标。




maSpotRow signature(object = "marrayNorm"): method which computes a vector of spot row coordinates for each spot.
maSpotRowsignature(object = "marrayNorm")方法计算现货行向量为每个点的坐标。




maSub signature(object = "marrayNorm"): slot accessor method.
maSubsignature(object = "marrayNorm")：插槽存取方法。




maSub<- signature(object = "marrayNorm"): slot assignment method.
maSub < - signature(object = "marrayNorm")：时隙分配方法。




maTargets signature(object = "marrayNorm"): slot accessor method.
maTargetssignature(object = "marrayNorm")：插槽存取方法。




maTargets<- signature(object = "marrayNorm", value = "marrayInfo"): slot assignment method.
maTargets < - signature(object = "marrayNorm", value = "marrayInfo")：时隙分配方法。




maW signature(object = "marrayNorm"): slot accessor method.
鱼肚signature(object = "marrayNorm")：插槽存取的方法。




maW<- signature(object = "marrayNorm", value = "matrix"): slot assignment method.
鱼肚< - signature(object = "marrayNorm", value = "matrix")：时隙分配方法。




print signature(x = "marrayNorm"): print method for "marrayNorm" class.
打印signature(x = "marrayNorm")："marrayNorm"类的打印方法。


作者（S）----------Author(s)----------


Sandrine Dudoit, <a href="http://www.stat.berkeley.edu/~sandrine">http://www.stat.berkeley.edu/~sandrine</a>.



参考文献----------References----------



参见----------See Also----------

marrayLayout, marrayRaw,
marrayLayout，marrayRaw


举例----------Examples----------


# Examples use swirl dataset, for description type ? swirl[例子使用漩涡集，描述的类型？漩涡]

data(swirl)

# Median normalization[中位数标准化]
mnorm<-maNorm(swirl[,2:3],norm="m")

# Object of class marrayNorm for the second and third swirl arrays[第二和第三的漩涡阵列类marrayNorm的对象]
mnorm

# Function call[函数调用]
maNormCall(mnorm)

#  Object of class marrayInfo -- Probe sequences[对象的类marrayInfo  - 探针序列]
maGnames(mnorm)

#  Object of class marrayInfo -- Target samples[对象的类marrayInfo  - 目标样本]
maTargets(mnorm)

# Density plot of log-ratios M for third array[log比密度积M为第三个数组]
plot(density(maM(mnorm[,2])), lwd=2, col=2, main="Density plots of log-ratios M")
lines(density(maM(swirl[,3])), lwd=2)
abline(v=0)
legend(2,1,c("Pre-normalization","Post-normalization"))

转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。


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