transform.madata(maanova)
transform.madata()所属R语言包：maanova
Micro Array experiment data transformation
微阵列实验数据转换
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This is the function to transform the Micro Array experiment data based on the given method.
这是函数变换的微阵列实验数据为基础在给定的方法。
用法----------Usage----------
## S3 method for class 'madata'
transform(`_data`,method=c("shift","glowess","rlowess","linlog","linlogshift"),
lolim, uplim, f=0.1, iter=3, degree=1, cg=0.3, cr=0.3, n.bin=10,
draw=c("screen", "dev", "off"), ...)
参数----------Arguments----------
参数：_data
An object of class madata.
对象类madata。
参数：method
The smoothing method.
平滑的方法。
参数：lolim
Low shift limit. If this argument is missing, the negative of the minimum element in the pmt data is used.
低转移的限制。如果缺少此参数，在PMT数据的最小元素的负面使用。
参数：uplim
High shift limit. If this argument is missing, the minimum element in the pmt data is used. lolim and uplim are applicable only if the method is "shift" or "linlogshift".
高转移的限制。如果缺少此参数，在PMT数据的最小元素。 lolim和uplim仅适用于该方法是“转变”或“linlogshift”。
参数：f
The smoother span. This gives the proportion of points in the plot which influence the smooth at each value. Larger values give more smoothness. It is equivalent to the "span" parameter in loess.
平滑的跨度。这给积点在每个值的影响顺利的比例。值越大，给更多的平滑。它是相当于“跨度”在loess参数。
参数：iter
The number of robustifying iterations which should be performed. Using smaller values of iter will make lowess run faster.
的稳健应执行的迭代数。使用ITER较小的值将LOWESS的运行速度。
参数：degree
The degree of the polynomials to be used in loess, up to 2. This is used when method is "glowess" or "rlowess".
用于黄土，最多2个，多项式的程度。这是时使用的方法是的“glowess”或“rlowess”。
参数：cg
Percentage of genes to be transformed linearly for the green channel.
基因的比例线性转化的绿色通道。
参数：cr
Percentage of genes to be transformed linearly for the red channel.
基因的比例线性转化为红色通道。
参数：n.bin
Number of bins for calculating the variance after linlogShift.
箱方差计算后linlogShift的数目。
参数：draw
Where to plot the transformation plots. "off" means no plot. "screen" means to display the plots on screen then x11() (in Unix/Windows) or macintosh() (in Mac) will be called inside the function. "dev" means to output the plots to the current device. User can use this option to output the plot to a file. Default option is "screen".
凡绘制的改造图。 “关”是指没有图。 “屏”是指显示在屏幕上的图X11（）（在Unix / Windows系统）或Macintosh（）（在Mac）将在函数内部调用。 “开发”是指当前设备输出的图。用户可以使用此选项，输出到一个文件中的图。默认选项是“屏幕”。
参数：...
Ignored at this point.
忽略这一点。
Details
详情----------Details----------
The smoothing methods include:
平滑的方法包括：
shift – the calculation of offset is based on the minimum sum of absolute deviations (SAD). Each array will have its own offset value. The data after shift cannot be smaller than 1.
转变 - 偏移计算绝对偏差最小和（SAD）的基础上。每个阵列将有其自己的偏移值。后移的数据不能小于1。
glowess – Intensity-based lowess. This method is to smooth the scatter plot of Ratio (R/G) versus Intensity (R*G). The formula in the fitting is ratio ~ intensity.
glowess - 基于强度LOWESS。这种方法是平滑的比率（的R / G）与强度（注册商标* g）的散点图。在拟合公式是比~强度。
rlowess – Joint lowess. This method is to smooth the scatter plot of Ratio versus Intensity and grid locations. It is the joint of intensity-based lowess and spatial loess. You have to have the grid location for every spot in order to use this method. The formula in fitting is ratio ~ intesity + row + col.
rlowess - 联合LOWESS。这种方法是平滑的比例与强度和网格位置的散点图。这是联合基于强度的的LOWESS和空间黄土。为了使用这种方法，你必须有每场的网格位置。在拟合公式是比~intesity +行+山坳。
linlog – Linear-log transformation.
linlog - 线性对数变换。
linlogshift – Linear-log shift transformation.
linlogshift - 线性log移位改造。
Previously, intensity lowess was called global lowess and joint lowess was called regional lowess. So I use "glowess" and "rlowess" in the method. Although the method names doesn't make too much sense, I will keep them for the reason of backward compatibility.
此前，强度LOWESS被称为全球LOWESS和联合的LOWESS被称为区域LOWESS。所以我用“glowess”和“rlowess”的方法。虽然方法名称不作太多的意义，我会保持向后兼容的原因。
If you have replicated spots and want to collapse them in read.madata by providing avgreps=1 or 2, you will lose grid information and joint lowess will be unavailable.
如果您已复制点和提供avgreps要崩溃read.madata= 1或2，你会失去电网的信息和联合LOWESS将无法使用。
Note that this function is only working for two-dye array.
请注意，此功能仅用于两染料阵列工作。
值----------Value----------
The return value is an object of class madata. Compared with the input object, the following fields are changed:
返回值是一个对象类madata。输入对象相比，改变以下领域：
Field data is the transformed data.
栏位data是转换后的数据。
Field TransformMethod will be the transformation method applied.
栏位TransformMethod将应用转化方法。
作者（S）----------Author(s)----------
Hao Wu
参考文献----------References----------
expression microarrays, Genetical Research, 77:123-128.
microarray data, Journal of Computational Biology, 7:819-837.
Microarray data, submitted, find manuscript in www.jax.org/research/churchill.
参见----------See Also----------
loess
loess
举例----------Examples----------
# load in data[数据加载]
data(kidney)
# do regional loess on raw data[对原始数据做区域的黄土]
## Not run: [＃无法运行：]
raw.lowess <- transform.madata(kidney.raw, method="rlowess")
graphics.off()
#do shift without displaying the plot [没有显示的图转变]
data1.shift <- transform.madata(kidney.raw, method="shift", lolim=-50,
uplim=50,draw="off")
# do global lowess and output the plots to a postscript file[全球LOWESS和输出的图PostScript文件]
postscript(file="glowess.ps")
data1.glowess <- transform.madata(kidney.raw, method="glowess", draw="dev")
graphics.off()
# do linear-log[做线性log]
data1.linlog <- transform.madata(kidney.raw, method="linlog")
graphics.off()
# do linear-log shift[做线性log移位]
data1.linlogshift <- transform.madata(kidney.raw, method="linlogshift",
lolim=-50, uplim=50)
graphics.off()
## 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 23:56:58
