dyebias.trendplot(dyebias)
dyebias.trendplot()所属R语言包：dyebias
Creates a trend-plot of all reporters, binned by dye bias, with all slides ordered by slide bias.
创建了所有记者的趋势图，染料偏见分级，与幻灯片偏置下令所有的幻灯片。
译者：生物统计家园网 机器人LoveR
描述----------Description----------
The aim of this routine is to show the monotonicity of the total dye bias in the (uncorrected) data set. This is to judge whether the total dye bias of one reporter in one hybridization indeed behaves as the product of an intrinsic gene specific dye bias (iGSDB) and a slide specific factor (the slide bias), which is at the heart of the GASSCO method.
这个程序的目的是显示单调（裸）数据集的总染料偏见。这是判断一个记者在一个杂交的总染料偏见的确作为一种内在的基因特异性染料偏见（iGSDB）和幻灯片的具体因素（幻灯片偏差），在的GASSCO方法的核心是产品的行为。
Showing the total dye bias of all reporters is too overwhelming, therefore the medians of the total dye bias after binning by intrinsic gene specific dye bias (as given in dyebias$dyebias) are
显示所有记者的总染料偏见是过于庞大，因此分级后，由内在基因特定的染料偏见总染料偏见的中位数（dyebias$dyebias）
用法----------Usage----------
dyebias.trendplot <- function(data, iGSDBs, dyebias.percentile=5, application.subset=TRUE,
n.bins=20,
type="median",
order,
output=NULL,
ylim=c(-2,2),
cex=0.3,
lty=1,
lwd=1,
main="dye bias trend plot",
xlab="slide bias rank",
ylab="M",
sub=NULL,
\dots)
参数----------Arguments----------
参数：data
The marrayNorm to trendplot.
marrayNorm趋势图。
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. Default should suffice in almost all cases.
内在基因特定的染料偏见（iGSDBs）突出记者的百分位。默认情况下应该足以在几乎所有情况下。
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：n.bins
The number of bins into which to classify the reporters, based on their intrinsic gene-specific dye bias. The median of each bin is plotted.
箱到其中的分类记者，根据其内在的特定基因的染料偏见。绘制每个bin中位数。
参数：type
What to print for each bin and hybridization. Valid values are:
如何打印每个bin和杂交。有效值是：
medianPlot the bin-median: the median of all genes in that bin and hybridization
medianPlot的bin中位数：在该垃圾箱中位数和所有基因杂交
meanPlot the mean of all genes in that bin and hybridization
所有的基因中，bin和杂交meanPlot平均
genePlot the single gene that has the lowest squared distance to the bin-median over all hybridizations
genePlot具有最低的距离平方所有杂交的bin位数的单基因
median.genePlot the single gene that has the median squared distance to the bin-medians over all hybridizations
median.genePlot所有杂交的bin-位数的中位数的平方距离的单基因
worst.genePlot the single gene that correlates worst with the bin-median over all hybridizations
worst.genePlot相关的bin中位数在所有杂交最差的单基因
参数：order
If order==NULL, the slides are sorted by increasing slide bias prior to boxplotting. This is typically done for data that is not yet dye bias corrected. This order is also returned as a value. If order!=NULL, the slides are put into this order before trendplotting. This is typically done for a dye bias-corrected data set, using the order of the uncorrected set.
如果order==NULL，幻灯片进行排序，增加幻灯片偏见到boxplotting前。这通常是尚未染料偏差纠正的数据。这个顺序也返回一个值。如果order!=NULL，幻灯片前trendplotting投入这个顺序。这通常是染料偏置校正数据集，使用裸集秩序。
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：ylim, lty, lwd, main, sub, cex, xlab, ylab
As for matplot()
matplot()
参数：...
Other arguments are passed on to matplot().
其他参数被传递到matplot()。
值----------Value----------
The order obtained, for use in a later call to this same function.
为了获得，在以后的调用此相同的功能使用。
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.monotonicity dyebias.monotonicityplot
dyebias.estimate.iGSDBs，dyebias.apply.correction，dyebias.rgplot，dyebias.maplot，dyebias.monotonicitydyebias.monotonicityplot
举例----------Examples----------
## show trend plots of uncorrected and corrected next to each other:[＃显示彼此相邻裸和纠正的趋势图：]
ylim <- c(-0.6, 0.6)
layout(matrix(1:2, nrow=1,ncol=2))
order <- dyebias.trendplot(data=data.norm,
iGSDBs=iGSDBs.estimated, # from e.g. dyebias.estimate.iGSDBs[从如dyebias.estimate.iGSDBs]
order=NULL, # i.e., order by increasing slide bias[即，为了增加幻灯片偏见]
output=NULL,
main="before correction",
ylim=ylim
)
order <- dyebias.trendplot(data=correction$data.corrected, # from dyebias.apply.correction[从dyebias.apply.correction]
iGSDBs=iGSDBs.estimated,
order=order, # order by the original slide bias[整理原始幻灯片偏见]
output=NULL,
main="after correction",
ylim=ylim
)
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 16:50:21
