Bscore(cellHTS)
Bscore()所属R语言包：cellHTS
B score normalization
乙得分标准化
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Correction of plate and spatial effects of the data xraw of a cellHTS object using the B score method. Using this method, a two-way median polish is fitted in a per-plate basis to account for row and column effects. Optionally, the obtained residuals within each plate can be further divided by their median absolute deviations to standardize for plate-to-plate variability. Optionally, a transformation to z-scores can be performed.
校正板和空间数据的影响xrawcellHTS对象，使用B的得分方法。使用这种方法，一个双向的中位数波兰被安装在每盘的基础上，行和列的效果。 （可选），每块板内获得的残差可以进一步划分由他们的平均绝对偏差，规范板对板的变异。可选的Z-分数的转换可以执行。
用法----------Usage----------
Bscore(x, what="xraw", adjustPlateMedian = TRUE, scale = TRUE, save.model = FALSE)
参数----------Arguments----------
参数：x
a cellHTS object that has already been configured. See details.
cellHTS已配置的对象。查看详情。
参数：what
a character indicating the slot of x to consider: "xraw" (default) or "xnorm".
字符指示槽x考虑："xraw"（默认）或"xnorm"。
参数：adjustPlateMedian
a logical value indicating whether the estimated average of each plate should also be substracted to the raw intensity values.
一个逻辑值，估计平均每盘是否也应加减的原始强度值。
参数：scale
a logical value indicating if the per-plate model residuals should be further scaled by their variance. See details.
一个逻辑值，指出如果每板模型的残差应该进一步的方差的比例。查看详情。
参数：save.model
a logical value specifying whether the per-plate models should be saved, and given as output. See details.
指定每板模型是否应该被保存，输出的逻辑值。查看详情。
Details
详情----------Details----------
The normalization is performed in a per-plate fashion using the B score method. This function can be called direclty, or indirectly, using normalizePlates or summarizeChannels. In the B score method, the residual r_{ijp} of the measurement for row i and column j on the p-th plate is obtained by fitting a two-way median polish, in order to account for both row and column effects within the plate:
使用B得分方法在每盘时尚标准化。此功能可以称为direclty或间接使用normalizePlates或summarizeChannels。在B的得分方法，剩余的r_{ijp}i和列j的P-TH板的连续测量，得到拟合双向位数波兰，以行和列的效果帐户内板块：
y_{ijp} is the measurement value in row i and column j of plate p (taken from x$xraw), and yest_{ijp} is the corresponding fitted value. This is defined as the sum between the estimated average of the plate (mu_p), the estimated systematic offset for row i (R_{ip}), and the systematic offset for column j (C_{jp}).
y_{ijp}是在连续测量值i和列板带够J（取自x$xraw），yest_{ijp}是相应的拟合值。这是我定义为估计平均之间的板（mu_p），行偏移估计系统的总和（R_{ip}），系统偏移j列（C_{jp}） 。
If scale=TRUE, for each plate p, each of the obtained residual values r_{ijp}'s are divided by the median absolute deviation of the residuals in plate p (MAD_p), giving the B score value:
如果scale=TRUE，P，每个所获得的剩余价值为每块板r_{ijp}的板P（残差中位数绝对偏差除以MAD_p），给了B的得分价值：
If adjustPlateMedian is set to FALSE, the estimated overall plate average (mu_p) is not removed from the intensity values y_{ijp}'s.
如果adjustPlateMedian设置为FALSE，估计整体板块平均（mu_p）从强度值y_{ijp}的删除。
If save.model=TRUE, the models residuals (r_{ijp}'s), row and column offsets and overall offsets are stored in the slots residuals, rowcol.effects and overall.effects of the cellHTS object x.
如果save.model=TRUE，模型残差（r_{ijp}的），行和列偏移和整体偏移存储在插槽residuals，rowcol.effects和overall.effects cellHTS对象x。
值----------Value----------
An object of class cellHTS, which is a copy of the argument x, plus an additional slot xnorm containing the normalized data. This is an array of the same dimensions as xraw. Furthermore, if save.model=TRUE, the slots residuals, rowcol.effects, and overall.effects (only if adjustPlateMedian was also set to TRUE) are added to x. The latter slots are arrays with the same dimension as x$xraw, except the overall.effects, which have dimensions 1 x nr Plates x nr Replicates x nr Channels.
cellHTS类的对象，这是一个参数的副本x，加上一个额外的插槽xnorm包含规范化的数据。这是一个xraw尺寸相同的数组。此外，如果save.model=TRUE，插槽residuals，rowcol.effects，overall.effects（只有adjustPlateMedian还设置TRUE）添加到x。后者的插槽为x$xraw同一维度的阵列，除了overall.effects，其中有尺寸1 x nr Plates x nr Replicates x nr Channels。
Moreover, the processing status of the cellHTS object is updated in the slot state to x$state["normalized"]=TRUE.
此外，处理cellHTS对象的状态更新插槽statex$state["normalized"]=TRUE。
作者（S）----------Author(s)----------
Ligia Braz <a href="mailto:ligia@ebi.ac.uk">ligia@ebi.ac.uk</a>
参考文献----------References----------
参见----------See Also----------
medpolish, plotSpatialEffects, normalizePlates, summarizeChannels
medpolish，plotSpatialEffects，normalizePlates，summarizeChannels
举例----------Examples----------
data(KcViabSmall)
x <- KcViabSmall
x <- Bscore(x, save.model = TRUE)
## identical result, but calling Bscore function from "normalizePlates"[＃相同的结果，但要求“normalizePlates”Bscore功能]
xopt <- normalizePlates(x, normalizationMethod="Bscore", save.model = TRUE)
all(x$xnorm==xopt$xnorm, na.rm=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。
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发表于 2012-2-25 14:20:14
