dyebias.rgplot(dyebias)
dyebias.rgplot()所属R语言包：dyebias
Produce scatterplots of the hybridization, with strongest dye
最强的染料生产的杂交散点图，
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Plots the $log_2(R)$ vs. $log_2(G)$ (or alternatively $M$ vs. $A$) signal of one slide, highlighting the reporters with the strongest red and green dye bias. Two lines indicate two-fold change. See also Margaritis et al. (2009), Fig. 1
图元log_2（R）的美元与$ log_2（G）的$（或者百万元$与$ $）信号的一个幻灯片，突出最强的红色和绿色的染料偏见的记者。两行表明两个方面的变化。看到也Margaritis等。 （2009年），图。 1
用法----------Usage----------
dyebias.rgplot(data, slide, iGSDBs, dyebias.percentile=5,
application.subset=TRUE, output=NULL,
xlim = c(log2(50),log2(50000)),
ylim = c(log2(50),log2(50000)),
xticks = c(100,1000,10000,10000),
yticks = c(100,1000,10000,10000),
pch = 19, cex = 0.3, cex.lab = 1.4,
\dots)
dyebias.maplot(data, slide, iGSDBs, dyebias.percentile=5,
application.subset=TRUE, output=NULL,
xlim = c(6,16), ylim = c(-2,2),
pch = 19, cex = 0.3, cex.lab = 1.4, \dots)
参数----------Arguments----------
参数：data
The marrayNorm object to plot one slide of.
marrayNorm对象绘制一张幻灯片。
参数：slide
The index of the slide to plot; must be > 1, and < maNsamples(data)
的图幻灯片指数;必须> 1，<maNsamples(data)
参数：iGSDBs
A data frame with intrinsic gene-specific dye biases, the same as that used in dyebias.apply.correction, probably returned by <br> dyebias.estimate.iGSDBs; see there for documentation.
可能具有内在的特定基因的染料偏见，在dyebias.apply.correction使用相同的数据框，返回参考dyebias.estimate.iGSDBs;看到那里的文档。
参数：dyebias.percentile
The percentile of intrinsic gene specific dye biases (iGSDBs) for which to highlight the reporters.
内在基因特定的染料偏见（iGSDBs）突出记者的百分位。
参数：application.subset
The set of reporters that was eligible for dye bias correction; same argument as for dyebias.apply.correction.
dyebias.apply.correction记者资格染料偏差校正;同样的论点。
参数：output
Specifies the output. If NULL, the existing output device is used; if output is one of "X11", "windows", "quartz", a new X11 (Unix)/windows (Windows)/quartz (Mac) device is created. If output is a string ending in one of ".pdf", ".png", ".eps", ".ps" is given, a file of that name and type is created and closed afterwards.
指定输出。如果NULL，现有输出设备的使用; output如果是"X11", "windows", "quartz"，一个新的X11（UNIX）/ /石英窗口（Windows）中（MAC）设备创建一个。 output如果是一个字符串“".pdf", ".png", ".eps", ".ps"给出一个文件，名称和类型的创建和关闭后结束。
参数：xlim,ylim, xticks, yticks,pch,cex,cex.lab
Graphical parameters; see par()
图形参数;看到par()
参数：...
Other arguments (such as main etc.) are passed on to plot().
其他参数（如main等）被传递到plot()。
值----------Value----------
None.
没有。
注意----------Note----------
The highlighted spots are all spots with an iGSDB that lies in the top- or bottom- dyebias.percentile of iGSDBS. That is, not just
强调点与一个iGSDB位于顶部或底部dyebias.percentileiGSDBS的所有点。也就是说，不只是
作者（S）----------Author(s)----------
Philip Lijnzaad <a href="mailto:p.lijnzaad@umcutrecht.nl">p.lijnzaad@umcutrecht.nl</a>
参考文献----------References----------
Kemmeren, P., van Hooff, S.R and Holstege, F.C.P. (2009). Adaptable gene-specific dye bias correction for two-channel DNA microarrays. Molecular Systems Biology, 5:266, 2009. doi: 10.1038/msb.2009.21.
参见----------See Also----------
dyebias.estimate.iGSDBs, dyebias.apply.correction, dyebias.rgplot, dyebias.maplot, dyebias.boxplot, dyebias.trendplot
dyebias.estimate.iGSDBs，dyebias.apply.correction，dyebias.rgplot，dyebias.maplot，dyebias.boxplot，dyebias.trendplot
举例----------Examples----------
## show both an RG-plot and an MA-plot of the uncorrected data and the[＃显示的RG-图和主图裸数据和]
## corrected data next to each other. [＃修正后的数据彼此相邻。]
slide <- 3 # or any other other, of course[或任何其他的，当然]
layout(matrix(1:4, nrow=2,ncol=2, byrow=TRUE))
dyebias.rgplot(data=data.norm,
slide=slide,
iGSDBs=iGSDBs.estimated, # from dyebias.estimate.iGSDBs[从dyebias.estimate.iGSDBs]
main=sprintf("RG-plot, uncorrected, slide %d", slide),
output=NULL)
dyebias.rgplot(data=correction$data.corrected,
slide=slide,
iGSDBs=iGSDBs.estimated,
main=sprintf("RG-plot, corrected, slide %d", slide),
output=NULL)
dyebias.maplot(data=data.norm,
slide=slide,
iGSDBs=iGSDBs.estimated,
main=sprintf("MA-plot, uncorrected, slide %d",slide),
output=NULL)
dyebias.maplot(data=correction$data.corrected,
slide=slide,
iGSDBs=iGSDBs.estimated,
main=sprintf("MA-plot, corrected, slide %d",slide),
output=NULL)
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。
|
发表于 2012-2-25 16:50:11
