stepWithinNorm(stepNorm)
stepWithinNorm()所属R语言包：stepNorm
Stepwise within-slide normalization function
逐步在幻灯片标准化功能
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This function conducts cDNA microarray normalization in a stepwise fashion. In a two-color cDNA array setting, within-slide normalization calibrates signals from the two channels to remove non-biological variation introduced by various processing steps.
此功能在一个循序渐进的方式进行cDNA微阵列标准化。在两色的cDNA阵列设置，幻灯片内标准化校准信号从两个渠道，删除非生物的变化推出不同的处理步骤。
用法----------Usage----------
stepWithinNorm(marraySet, subset=TRUE, wf.loc, criterion = c("BIC", "AIC"), loss.fun = square)
参数----------Arguments----------
参数：marraySet
Object of class marrayRaw or class marrayNorm, containing intensity data for the batch of arrays to be normalized.
类marrayRaw或类对象marrayNorm为一批阵列，包含强度数据进行标准化。
参数：subset
A "logical" or "numeric" vector indicating the subset of points used to compute the normalization values.
“逻辑”或“数字”向量表示用来计算标准化值点的子集。
参数：wf.loc
Object of class list, each component is a step for the removal of a particular systematic variation. Typically each step is also a list of several candidate models of different complexity, the best model will be chosen by the criterion specified. For a user friendly way of constructing such a list, consult the function makeStepList.If missing, the default procedure will be used, which we consider appropriate for most slides. See details for how to specify the list and how it is used.
对象类list，每个组件是去除特定系统的变化的一个步骤。通常情况下，每一步也是不同复杂性的几个候选车型名单，将选择最好的模式，由criterion指定。对于一个用户友好的方式来构建这样一个列表，咨询的功能makeStepList如果缺少，默认的程序将被使用，我们认为这适合于大多数幻灯片。请参阅如何指定列表的详细信息，以及如何使用它。
参数：criterion
Character string specifying the criterion used for the selection of the best normalization procedure in each step. This argument can be specified using the first letter of each method; if no specification is made, the default is BIC:
字符串指定用于最好的标准化过程中每一步的选择标准。这种说法，可以指定使用的每一种方法的第一个字母;如果没有规范，是默认的BIC：
AIC:the AIC criterion is used
工商局：AIC准则
BIC:the BIC criterion is used.
的BIC BIC准则。
参数：loss.fun
loss function; default set at using residual sum of squares.
默认情况下，使用残差平方和损失函数;集。
Details
详情----------Details----------
Typical systematic non-biological variations of a two-color cDNA microarray include the dependence of ratio measurements (M) on intensity (A), print-tip IDs (PT), plate IDs (PL) and spatial heterogeneity of the slide (SP). The stepwise normalization procedure normalizes a slide in a stepwise fashion. In each step one kind of variation is targeted for correction. Within each step, various candidate models are assessed for their adequacy with respect to the observed data. The assessment is made based on a common model selection criterion, AIC (see calcAIC) or BIC (see calcBIC), and the best model is then chosen for the specified step.
典型系统的非生物两色的cDNA微阵列的变化，包括依赖强度比测量（男）（一），打印头标识（PT），标识板（PL）和幻灯片的空间异质性（SP） 。逐步标准化过程标准化在逐步时尚的幻灯片。在每一步中的一种变异有针对性的改正。在每一步中，各候选机型进行评估，他们观测到的数据是否足够。评估是由一个共同的模型甄选准则的基础上，工商局（见calcAIC）或BIC（见calcBIC），最好的模式，然后选择指定步。
The argument wf.loc is a list of steps. Each step is also a list of models. The user uses the function fitWithin or fit2DWithin to specify a model. Below is a table of how to do so:
参数wf.loc是一个步骤的列表。每一个步骤，也是一个型号的列表。用户使用的功能fitWithin或fit2DWithin指定一个模型。以下是如何做到这一点的表：
If the wf.loc is not specified by the user, the default procedure conducts normalization in four steps: A -> PT -> PL -> SP and models are as described in the table above. The user can choose not to follow such a procedure by passing in a different list, however we advocate normalizing the intensity (A) variation first as it is usually the source of most variation in most slides. The list can be easier specified using the function makeStepList by inputing models as character strings, see makeStepList for details.
如果wf.loc不是由用户指定，默认的程序进行标准化四个步骤： - > PT - >的PL - > SP和模型在上述表中所述。用户可以选择不遵循这样一个过程，通过在不同的列表，但是我们主张标准化的强度（A）的变化第一，因为它通常是最变化最幻灯片的来源。该列表可以指定使用功能makeStepList通过输入查询的字符串模型，看到makeStepList详情。
值----------Value----------
An object of class "list":
一个对象类“列表”：
参数：normdata
an object of class marrayNorm, containing the normalized intensity data.
类marrayNorm的对象，包含归强度数据。
参数：res
a dataframe of the stepwise normalization result, containing the name of the model chosen for each step, deviance, equivalent number of parameters, AIC/BIC value.
的dataframe逐步标准化结果的，包含的每一步，偏差，同等数量的参数，工商行政管理机关/ BIC的值选择模型的名称。
作者（S）----------Author(s)----------
Yuanyuan Xiao, <a href="mailto:yxiao@itsa.ucsf.edu">yxiao@itsa.ucsf.edu</a>, <br>
Jean Yee Hwa Yang, <a href="mailto:jean@biostat.ucsf.edu">jean@biostat.ucsf.edu</a>
参考文献----------References----------
for cDNA microarray data. In M. L. Bittner, Y. Chen, A. N. Dorsel, and E. R. Dougherty (eds), Microarrays: Optical Technologies and Informatics, Vol. 4266 of Proceedings of SPIE.
(2003). New normalization methods for cDNA microarray data. Bioinformatics, Vol. 19, pp. 1325-1332.
参见----------See Also----------
seqWithinNorm, withinNorm, fitWithin, fit2DWithin,
seqWithinNorm，withinNorm，fitWithin，fit2DWithin
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)
# Apply stepwise normalization for the first slide[申请第一张幻灯片的逐步标准化]
res.swirl1 <- stepWithinNorm(swirl[,1])
# normalized data[规范化的数据]
norm.swirl <- res.swirl1[[1]]
# stepwise procedure[逐步程序]
step.swirl <- res.swirl1[[2]]
# using a stepwise procedure different than the default[使用一个循序渐进的过程，而不是默认不同]
# corrects intensity (A) and print-tip (PT), this can be[纠正强度（A）和打印头（PT），这可能是]
# carried out in two ways:[进行了两种方式：]
# 1)[1）]
steps <- list(
wholeChipA = list(med = fitWithin(fun="medfit"),
rlm = fitWithin(fun="rlmfit"),
loess = fitWithin(fun="loessfit")),
printTipA = list(med = fitWithin(z.fun="maPrintTip", fun="medfit"),
rlm = fitWithin(z.fun="maPrintTip", fun="rlmfit"),
loess = fitWithin(z.fun="maPrintTip",fun="loessfit")))
#2) [2）]
steps <- makeStepList(PL=NULL, Spatial2D=NULL)
## Not run: [＃无法运行：]
res.swirl <- stepWithinNorm(swirl[,1], wf.loc=steps)
## End(Not run)[＃结束（不运行）]
# using AIC criterion for the first slide[第一张幻灯片使用AIC准则]
## Not run: [＃无法运行：]
res.swirl <- stepWithinNorm(swirl[,1], criterion="A")
## 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 2012-2-26 15:12:29
