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

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

                                        Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
                                         类“marrayRaw”类和标准化前的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 pre-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 green (Cy3) and red (Cy5) foreground and background intensities, the layout of the arrays, and descriptions of the target samples hybridized to
这个类代表的一批基因芯片标准化前的强度数据。一批阵列组成具有相同的布局（"marrayLayout"）数组的集合。这个类包含的绿色（Cy3标记）和红色（Cy5标记）的前景和背景强度，阵列的布局，杂交的目标样本的描述插槽


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

Objects can be created by calls of the form    new('marrayRaw',<br>     maRf      = ...., # Object of class matrix<br>     maGf      = ...., # Object of class matrix<br>     maRb      = ...., # Object of class matrix<br>     maGb      = ...., # 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>   )
可以创建对象调用的形式  new('marrayRaw',参考    maRf      = ...., # Object of class matrix参考    maGf      = ...., # Object of class matrix参考    maRb      = ...., # Object of class matrix参考    maGb      = ...., # 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  )


插槽----------Slots----------




maRf: Object of class "matrix", red foreground intensities, rows correspond to spotted probe sequences, columns to arrays in the batch.
maRf类"matrix"，红色前景强度，行对应斑点探针序列，批次中的数组的列对象。




maGf: Object of class "matrix", green foreground intensities, rows correspond to spotted probe sequences, columns to arrays in the batch.
maGf类"matrix"，绿色的前景强度，行对应斑点探针序列，批次中的数组的列对象。




maRb: Object of class "matrix", red background intensities, rows correspond to spotted probe sequences, columns to arrays in the batch.
maRb：对象类"matrix"，红色背景的强度，行对应斑点探针序列，列在批次阵列。




maGb: Object of class "matrix", green background intensities, rows correspond to spotted probe sequences, columns to arrays in the batch.
maGb：对象类"matrix"，绿色背景的强度，行对应斑点探针序列，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 the 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。


方法----------Methods----------




[ signature(x = "marrayRaw"): subsetting operator for spots on the array and arrays in the batch, ensures that all slots are subset properly.
[signature(x = "marrayRaw")：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 = "marrayRaw"): function which computes average log-intensities (base 2) A for an object of class "marrayRaw".
的MAAsignature(object = "marrayRaw")：计算平均为对象的类"marrayRaw"登录强度（碱基）的功能。




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




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




maGb signature(object = "marrayRaw"): slot accessor method.
maGbsignature(object = "marrayRaw")：插槽存取方法。




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




maGb<- signature(object = "marrayRaw", value = "NULL"): slot assignment method.
maGb < - signature(object = "marrayRaw", value = "NULL")：时隙分配方法。




maGf signature(object = "marrayRaw"): slot accessor method.
maGfsignature(object = "marrayRaw")：插槽存取方法。




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




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




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




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




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




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




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




maLG signature(object = "marrayRaw"): method which computes green log-intensities (base 2) for an object of class "marrayRaw".
maLGsignature(object = "marrayRaw")方法，计算为一个对象类"marrayRaw"绿色登录强度（基数为2）。




maLR signature(object = "marrayRaw"): method  which computes red log-intensities (base 2) for an object of class "marrayRaw".
maLRsignature(object = "marrayRaw")：方法计算对象类"marrayRaw"红log强度（基数为2）。




maM signature(object = "marrayRaw"): method which computes intensity log-ratios (base 2) M for an object of class "marrayRaw".
MAMsignature(object = "marrayRaw")方法计算强度为对象类"marrayRaw"数比率（基数2）男。




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




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




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




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




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




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




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




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




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




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




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




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




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




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




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




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




maRb signature(object = "marrayRaw"): slot accessor method.
maRbsignature(object = "marrayRaw")：插槽存取方法。




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




maRb<- signature(object = "marrayRaw", value = "NULL"): slot assignment method.
maRb < - signature(object = "marrayRaw", value = "NULL")：时隙分配方法。




maRf signature(object = "marrayRaw"): slot accessor method.
MARFsignature(object = "marrayRaw")：插槽存取方法。




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




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




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




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




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




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




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




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




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




print signature(x = "marrayRaw"):  print method for "marrayRaw" class.
打印signature(x = "marrayRaw")："marrayRaw"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, marrayNorm, marrayInfo.
marrayLayout，marrayNorm，marrayInfo。


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]
require(limma)
data(swirl)

# Object of class marrayRaw for the 4 swirl arrays[4涡流阵列类marrayRaw的对象]
swirl

# Object of class marrayLayout[对象类marrayLayout的]
maLayout(swirl)

# Access only the first 100 spots of the third array[只有进入第三个数组的第一个100点]
swirl[1:100,3]

# Accessor methods -- How many spots on the array[存取方法 - 多少点阵列]
maNspots(swirl)

# Density plot of log-ratios M for third array[log比密度积M为第三个数组]
plot(density(maM(swirl[,3])))

# Assignment methods -- Replace maNotes slot[分配方法 - 更换maNotes插槽]
maNotes(swirl)
maNotes(swirl)<-"This is a zebrafish microarray"
maNotes(swirl)

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


注：
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