plot.qc.stats(simpleaffy)
plot.qc.stats()所属R语言包：simpleaffy
Plots a QCStats object
绘制QCStats对象
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Generates a visual summary of the various QC statistics recommended by Affymetrix in their 'Data Analysis Fundamentals' handbook.
由Affymetrix公司在他们的“数据分析基础知识”手册建议的各种QC统计生成的视觉总结。
参数----------Arguments----------
参数：x
A QCStats object
一个QCStats对象
参数：fc.line.col
The colour to mark fold change lines with
颜色标记倍线
参数：sf.ok.region
The colour to mark the region in which scale factors lie within appropriate bounds
颜色标示的区域，其中规模因素在于在适当的范围内
参数：chip.label.col
The colour to label the chips with
颜色标签芯片
参数：sf.thresh
Scale factors must be within this fold-range
规模因素必须是这个倍范围内
参数：gdh.thresh
Gapdh ratios must be within this range
GAPDH的比值必须在此范围内
参数：ba.thresh
beta actin must be within this range
肌动蛋白测试必须在此范围内
参数：present.thresh
The percentage of genes called present must lie within this range
被称为目前的基因的百分比必须位于此范围内
参数：bg.thresh
Array backgrounds must lie within this range
阵列背景必须位于此范围内
参数：label
What to call the chips
叫什么芯片
参数：main
The title for the plot
图的标题
参数：usemid
If true use 3'/M ratios for the GAPDH and beta actin probes
如果真正使用3 / M比GAPDH和β肌动蛋白探针
参数：cex
Value to scale character size by (e.g. 0.5 means that the text should be plotted half size)
值缩放字符的大小（如0.5表示该文本应策划的一半大小）
参数：...
Other parameters to pass through to plot
其他参数，通过plot
Details
详情----------Details----------
A lot of information is presented in this one figure. By default, each array is represented by a seperate line in the figure. The central vertical line corresponds to 0 fold change, the dotted lines on either side correspond to 3 fold up and down regulation. The blue bar represents the region in which all arrays have scale factors within, by default, three-fold of each other. Its position is found by calculating the mean scale factor for all chips and placing the center of the region such that the borders are -1.5 fold up or down from the mean value.
大量的信息，提出在这一个数字。默认情况下，每个阵列是由单独的线路图中代表。中央垂直线对应0倍的变化，两边的虚线对应到3倍最高下调。蓝色条代表在哪个区域所有阵列有规模的因素，在默认情况下，对方的3倍。通过计算所有芯片平均规模因素和配售中心的区域，如边界-1.5倍或平均值，其位置被发现。
Each array is plotted as a line from the 0-fold line to the point that corresponds to its scale factor. If the ends of all of the lines are in the blue region, their scale-factors are compatible. The lines are coloured blue if OK, red if not.
每个阵列作为一个从0倍线到其规模因素对应的点线绘制。如果在蓝色区域是所有线路的两端，其规模因素是兼容的。线条如果OK，红色，如果不蓝色。
The figure also shows GAPDH and beta-actin 3'/5' ratios. These are represented as a pair of points for each chip. Affy state that beta actin should be within 3, gapdh around 1. Any that fall outside these thresholds (1.25 for gapdh) are coloured red; the rest are blue.
该图还显示GAPDH和β-肌动蛋白3/5的比例。这些代表对每个芯片作为一个点。 affy状态，β肌动蛋白应在约1 3，GAPDH。任何超出这些阈值下降（GAPDH 1.25）是红色的，其余的都是蓝色。
Written along the left hand side of the figure are the number of genes called present on each array and the average background. These will vary according to the samples being processed, and Affy's QC suggests simply that they should be similar. If any chips have significantly different values this is flagged in red, otherwise the numbers are displayed in blue. By default, 'significant' means that %-present are within 10% of each other; background intensity, 20 units. These last numbers are somewhat arbitrary and may need some tweaking to find values that suit the samples you're dealing with, and the overall nature of your setup.
书面沿左侧的数字是每个阵列和平均背景上称为基因。这些将根据正在处理的样品，Affy的QC只是说，他们应该是类似的建议。如果任何芯片有显着不同的价值观，这是红色的标记，否则这些数字都显示为蓝色。默认情况下，重大的意思是在对方的10％％，目前的背景强度，20个单位。这些最后的数字是有点乱，可能需要一些调整，以找到适合你的样品处理，设置的整体性质的值。
Finally, if BioB is not present on a chip, this will be flagged by printing 'BioB' in red.
最后，如果BioB是在一个芯片上不存在，这将是通过打印BioB红色的标记。
In short, everything in the figure should be blue - red highlights a problem!
总之，图中的一切应该是蓝色的，红色的亮点 - 一个问题！
用法----------Usage----------
<p>plot.qc.stats(x, fc.line.col = "black", sf.ok.region = "light blue", chip.label.col = "black", sf.thresh = 3, gdh.thresh = 1.25, ba.thresh = 3, present.thresh = 10, bg.thresh = 20, label = NULL,title="QC Stats",spread=c(-8,8),usemid=F,type="l",cex=1, ...)
</p>
作者（S）----------Author(s)----------
Crispin J Miller
参见----------See Also----------
qc
qc
举例----------Examples----------
data(qcs)
plot(qcs)
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 2012-2-26 14:21:26
