qa3prime(ArrayTools)
qa3prime()所属R语言包：ArrayTools
Creating Quality Assessment Report for 3 Prime Array
创建3首要阵列的质量评估报告
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Creating Quality Assessment Report for 3 Prime Array in HTML file
创建质量3阵列首要在HTML文件的评估报告
用法----------Usage----------
qa3prime(object, parameters, outputFile = "QA.html", mydir = getwd())
参数----------Arguments----------
参数：object
an AffyBatch object
AffyBatch对象
参数：parameters
The names of the variables to be included in the report
变量的名字被列入报告中
参数：outputFile
The name of the outputfile. Make sure write ".html"
名称的OUTPUTFILE。确保写“HTML”。
参数：mydir
The name of the directory containing the report
目录的名称包含报表
Details
详情----------Details----------
This function creates quality control report in an HTML file that contains a set of 9 assessment figures.
这个函数创建一个HTML文件，它包含了一套9评估数字质量控制报告。
Figure1: The Raw Intensity Plot. The raw intensity should be similar across all chips
图1：原始强度图。原始强度应该在所有芯片类似
Figure2: The Average Background/Percentage Present Plot. The Average Background should be similar across all chips. The Percentage Present should be similar across all chips, except that in rare situations transcription is globally shut down or turned on under some conditions
图2：平均的背景/百分比的现状图。平均的背景应该是所有芯片类似。百分比目前应该是所有芯片相似，除了在极少数情况下转录是全球关闭或关闭，在一定条件下
Figure3: The Scaling Factor Plot. The scaling factor should be within 3-fold across all chips
图3：比例因子图。比例因子应该在所有芯片的3倍
Figure4: The Hybridization Controls Plot. BioB, BioC, BioD, CreX should be called present, except that it is acceptable if BioB is absent sometimes.
图4：杂交控制图。 ，CREX BioB，BioC，BIOD应称为目前，除了它是可以接受的，如果BioB有时缺席。
Figure5: The Housekeeping Controls Plot. The GAPDH ratio should be around 1 and the actin ratio should be less than 3. Note that if two-cycle amplification or NuGen amplification is used, this ratio could be much higher.
图5：家政控制图。 GAPDH的比例应该在1和肌动蛋白的比例应小于3。请注意，如果使用两个周期放大或NuGen的放大，这个比例可能会高得多。
Figure6: The RNA Degradation Plot. On Affymetrix GeneChips, individual probes in a probeset are ordered by location relative to the 5' end of the targeted RNA molecule. On each chip, probe intensities are averaged by location in the probeset, with the average taken over probesets. In an RNA digestion plot, these means are plotted side-by-side, making it easy to notice any 5' to 3' trend. The trend can be due to RNA degradation or 3'-biased amplification. Since RNA degradation typically starts from the 5' end of the molecule and amplification starts at the 3' end, we would expect probe intensities to be systematically lowered at the 5' end of a probeset when compared to the 3' end.
图6-1：RNA降解图的。在Affymetrix基因芯片，个别探针在probeset下令针对性的RNA分子的5端的相对位置。每个芯片上，探针强度平均位置在probeset，与超过probesets平均。在RNA消化图，这些手段绘制端侧，很容易地发现任何5至3趋势。可能是由于RNA降解或3-偏见放大的趋势。由于RNA的降解通常分子的5端启动和放大开始在3端，我们希望系统在5探针强度降低“probeset结束时相比，3端。
Figure7: The Hierarchical Clustering of Samples. Samples will be grouped using hierarchical clustering and principal component analysis (PCA). If the sample preparation steps introduced bigger variation than biological variation, treatment groups will be mixed up in the plot. This could also happen when the samples between groups were mixed up accidentally when the samples were prepared. We acknowledge that clinical samples are harder to collect and sometimes impossible to control. Therefore, sample QC criteria will be much looser when dealing with clinical samples.
图7：样本层次聚类。样品将采用分层聚类和主成分分析（PCA）进行分组。如果样品制备步骤介绍大于变异生物的变化，治疗组将混在图。这也可能发生，当群体之间的样品混合时意外的样品制备。我们承认，临床样本难以收集，有时无法控制。因此，样品的质量控制标准，将是非常宽松的处理临床样品时。
Figure8: The Pseudo-chip Images. A Pseudo-chip image plots the weights and residuals from the model fit. The image plot allows detection of artifacts on the chip.
图8-3：伪芯片的图像。伪芯片的图像图的重量，并从模型的拟合残差。图像的图，使检测芯片上的文物。
Figure9: The Normalized Unscaled Standard Error (NUSE) and Relative Log Expression (RLE) Plots. The NUSE is fitted robustly by iteratively reweighted least squares (IRLS) so that the standard error of the estimated log2 scale expression can be estimated. The boxplots of the NUSE show the differences in hybridization quality most clearly, in magnitude as well as variability. A high NUSE likely corresponds to a low signal. The RLE plot is a boxplot showing the distribution of Log2 ratio of each chip relative to a median chip. A discordant distribution infers a problem with the chip.
图9-2：归未缩放的标准错误（怒色）和相对log表达（RLE）图。迭代加权最小二乘（IRLS），这样的标准误差估计的log2规模表达可估计的怒色装有强劲。怒色的盒状图显示杂交质量的差异，最清楚的是，在数量，以及变异。高怒色可能相对低信号。 RLE的图是一个盒形图显示的log2每个芯片相对比的分布中位数芯片。一个不和谐的分布推断与芯片的一个问题。
值----------Value----------
no value is returned
没有返回值
作者（S）----------Author(s)----------
Xiwei Wu, Arthur Li
参考文献----------References----------
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 12:22:14
