qaGeneST(ArrayTools)
qaGeneST()所属R语言包：ArrayTools
Creating Quality Assessment Report for Gene ST Array
建立质量评估报告基因ST阵列
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Creating Quality Assessment Report for Gene ST Array in HTML file
创建基因ST阵列在HTML文件的质量评估报告
用法----------Usage----------
qaGeneST(object, parameters, QC, mydir = getwd(), outputFile = "QA.html")
参数----------Arguments----------
参数：object
an ExpressionSet
ExpressionSet
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：QC
The QC report generated from Affymetrix Expression Console
从Affymetrix的表达控制台产生的QC报告
参数：mydir
The name of the directory containing the report
目录的名称包含报表
参数：outputFile
The name of the outputfile. Make sure write ".html"
名称的OUTPUTFILE。确保写“HTML”。
Details
详情----------Details----------
This function creates quality control report in an HTML file that contains a set of 8 assessment figures.
这个函数创建一个HTML文件，它包含了一套8评估数字质量控制报告。
Figure1: The intensity distributio Plot. The raw intensity should be similar across all chips
图1：强度分布图。原始强度应该在所有芯片类似
Figure2: The Mean Signal Plot. The mean signal of each group should be consistant across the samples. The positive control should be higher than the negative controls.
图2：平均信号图。平均每个组的信号，应该是整个样本洽场。阳性对照应高于阴性对照。
Figure3: BAC SPIKE plot. The mean signal of each group should be consistant across the samples. The signal for BioB should be the lowest, follows by BioC, BioD, and CreX (the highest).
图3：BAC穗积。平均每个组的信号，应该是整个样本洽场。为BioB的信号应该是最低的，，由BioC，BIOD，CREX（最高）。
Figure4: POLYA SPIKE plot. The mean signal of each group should be consistant across the samples. The signal for Lys should be the lowest, follows by Thr, Phe, and Dap.
图4：波利亚穗积。平均每个组的信号，应该是整个样本洽场。赖氨酸信号应该是最低的，由苏氨酸，苯丙氨酸和DAP如下。
Figure5: POS VS NEG AUC plot. Pos vs neg auc is the area under the curve (AUC) for a receiver operating characteristic (ROC) plot comparing signal values for the positive controls to the negative controls. In practice the expected value for this metric is tissue type specific and may be sensitive to the quality of the RNA sample. Values between 0.80 and 0.90 are typical.
图5：POS VS南德的AUC图。 POS与NEG AUC曲线下面积（AUC）为受试者工作特征（ROC）为阴性对照，阳性对照比较信号值的图。在实践中，这个度量的预期值是特定的组织类型和可能是敏感的RNA样品的质量。 0.80和0.90之间的值是典型的。
Figure6: MAD RESIDUAL MEAN plot. A measure of how well or poor all of the probes on a given chip fit the RMA or PLIER model. An unusually high mean absolute deviation of the residuals from the median suggests problematic data for that chip.
图6-1：MAD残余均值图。如何好或差一个给定的芯片上的探针适合RMA或钳模型的度量。一个异常高的平均绝对偏差残差中位数，表明该芯片有问题的数据。
Figure7: RLE MEAN plot. This metric is generated by taking the signal estimate for a given probeset on a given chip and calculating the difference in log base 2 from the median signal value of that probeset over all the chips. When just the replicates are analyzed together the mean absolute RLE should be consistently low, reflecting the low biological variability of the replicates.
图7：RLE的均值图。该指标所产生的信号估计一个给定的一个给定的芯片和probeset计算在log碱基2个，超过所有芯片probeset信号值中位数的差异。当只是在重复一起进行分析的平均绝对RLE的应该是一直很低，反映了低生物变异的复制。
Figure8: 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8-3：样品的层次聚类。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。
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 12:22:33
