normalizeForPrintorder(limma)
normalizeForPrintorder()所属R语言包：limma
Print-Order Normalization
打印秩序标准化
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Normalize intensity values on one or more spotted microarrays to adjust for print-order effects.
标准化的一个或多个斑点芯片来调整打印顺序效应强度值。
用法----------Usage----------
normalizeForPrintorder(object, layout, start="topleft", method = "loess", separate.channels = FALSE, span = 0.1, plate.size = 32)
normalizeForPrintorder.rg(R, G, printorder, method = "loess", separate.channels = FALSE, span = 0.1, plate.size = 32, plot = FALSE)
plotPrintorder(object, layout, start="topleft", slide = 1, method = "loess", separate.channels = FALSE, span = 0.1, plate.size = 32)
参数----------Arguments----------
参数：object
an RGList or list object containing components R and G which are matrices containing the red and green channel intensities for a series of arrays
RGList或list对象，其中包含组件R和G这是矩阵包含了一系列阵列的红色和绿色通道强度
参数：R
numeric vector containing red channel intensities for a single microarray
数字向量包含一个单一的芯片红色通道强度
参数：G
numeric vector containing the green channel intensities for a single microarray
数字向量单一芯片的绿色通道强度
参数：layout
list specifying the printer layout, see PrintLayout-class
列出指定打印机布局，看到PrintLayout-class
参数：start
character string specifying where printing starts in each pin group. Choices are "topleft" or "topright".
字符串指定的印刷开始在每个引脚组。选择是"topleft"或"topright"。
参数：printorder
numeric vector specifying order in which spots are printed. Can be computed from printorder(layout,start=start).
数字矢量指定顺序点打印。可以计算从printorder(layout,start=start)。
参数：slide
positive integer giving the column number of the array for which a plot is required
正整数的要求，其中有一个图是阵列的列数
参数：method
character string, "loess" if a smooth loess curve should be fitted through the print-order trend or "plate" if plate effects are to be estimated
字符串，“黄土”如果顺利黄土曲线应通过打印命令趋势或“盘子”装板效果估计
参数：separate.channels
logical, TRUE if normalization should be done separately for the red and green channel and FALSE if the normalization should be proportional for the two channels
逻辑，TRUE如果标准化应为红色和绿色通道分别FALSE如果标准化应该是成正比的两个通道
参数：span
numerical constant between 0 and 1 giving the smoothing span for the loess the curve. Ignored if method="plate".
黄土曲线平滑跨度0和1之间的数值不变。如果method="plate"忽略。
参数：plate.size
positive integer giving the number of consecutive spots corresponding to one plate or plate pack. Ignored if method="loess".
连续点的数量，相应的一板或板片的正整数。如果method="loess"忽略。
参数：plot
logical. If TRUE then a scatter plot of the print order effect is sent to the current graphics device.
逻辑。如果TRUE然后打印命令的效果散点图被发送到当前图形设备。
Details
详情----------Details----------
Print-order is associated with the 384-well plates used in the printing of spotted microarrays. There may be variations in DNA concentration or quality between the different plates. The may be variations in ambient conditions during the time the array is printed.
打印顺序与发现芯片的印刷所用的384孔板。有可能在不同板块之间的DNA浓度或质量的变化。可能是在阵列打印时环境条件的变化。
This function is intended to pre-process the intensities before other normalization methods are applied to adjust for variations in DNA quality or concentration and other print-order effects.
此功能的目的是预先处理的强度之前，其他标准化方法应用于调整DNA的质量或浓度的变化和其他的打印顺序的影响。
Printorder means the order in which spots are printed on a microarray. Spotted arrays are printed using a print head with an array of print-tips. Spots in the various tip-groups are printed in parallel. Printing is assumed to start in the top left hand corner of each tip-groups and to proceed right and down by rows, or else to start in the top right hand and to proceed left and down by rows. See printorder for more details. (WARNING: this is not always the case.) This is true for microarrays printed at the Australian Genome Research Facility but might not be true for arrays from other sources.
printorder是指在一个芯片上印点的顺序。斑点阵列打印使用打印头与打印提示数组。尖在各组的景点是印在平行。假设在每个尖组顶端的左上角开始向右和向下按行进行，或者在顶端的右手，并着手开始向左和向下按行打印。看到printorder更多细节。 （警告：这是情况并非总是如此），这是真正的印在澳大利亚基因组研究基金的芯片，但未必真正从其他来源的阵列。
If object is an RGList then printorder is performed for each intensity in each array.
如果object是一个RGList然后printorder每个阵列中的每个强度进行。
plotPrintorder is a non-generic function which calls normalizeForPrintorder with plot=TRUE.
plotPrintorder是一个非泛型函数调用normalizeForPrintorderplot=TRUE。
值----------Value----------
normalizeForPrintorder produces an RGList containing normalized intensities.
normalizeForPrintorder生产RGList归强度。
The function plotPrintorder or normalizeForPrintorder.rg with plot=TRUE returns no value but produces a plot as a side-effect.
函数plotPrintorder或normalizeForPrintorder.rg用plot=TRUE没有返回值，但产生一个小区作为一个副作用。
normalizeForPrintorder.rg with plot=FALSE returns a list with the following components:
normalizeForPrintorder.rgplot=FALSE返回一个与以下组件：
参数：R
numeric vector containing the normalized red channel intensities
数字向量归红色通道强度
参数：G
numeric vector containing the normalized red channel intensites
数字向量，规范化的红色通道intensites
参数：R.trend
numeric vector containing the fitted printorder trend for the red channel
数字向量的红色通道的的拟合printorder趋势
参数：G.trend
numeric vector containing the fitted printorder trend for the green channe
数字向量的绿色channe的的拟合printorder趋势
作者（S）----------Author(s)----------
Gordon Smyth
参考文献----------References----------
参见----------See Also----------
printorder.
printorder。
An overview of LIMMA functions for normalization is given in 05.Normalization.
在05.Normalization标准化LIMMA功能概述。
举例----------Examples----------
## Not run: [＃无法运行：]
# This example is designed for work on a subset of the data[这个范例是专为数据的一个子集的工作]
# from the ApoAI case study in Limma User's Guide[载脂蛋白AI在Limma用户指南案例研究]
# This example was formerly loaded from sma package using[这个例子是以前从SMA使用包装]
# library(sma)[库（SMA）]
# data(MouseArray)[数据（MouseArray）]
plotPrintorder(mouse.data,mouse.setup,slide=1,separate=TRUE)
RG <- normalizeForPrintorder(mouse.data,mouse.setup)
## 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 2012-2-25 23:20:09
