ABarray(ABarray)
ABarray()所属R语言包：ABarray
Utility to perform QA, data transformation and statistical analysis
实用程序来执行的质量保证，数据转换和统计分析
译者：生物统计家园网 机器人LoveR
描述----------Description----------
(1) Read output from AB1700 software output; (2) Create raw data QA and associated plots including boxplot, control data signal plot; (3) Missing value calculation; (4) Create MA, scatter plot; (5) Perform quantile normalization; (6) Perform t test and fold change, or ANOVA (using separate function if more than 2 subgroups). (7) Create heatmap with hierarchical clustering. (8) The results are either in graphics or text files.
（1）阅读AB1700软件输出的输出;（2）创建原始数据的质量保证和相关的图，包括盒形图，控制数据信号图;（3）缺少值的计算;（4）建立马，散点图;（5）执行位数标准化（6）执行t检验和褶皱的变化，或方差分析（使用单独的功能，如果超过2个亚组）。 （7）创建层次聚类的热图。 （8）结果是在图形或文本文件。
用法----------Usage----------
ABarray(dataFile, designFile, group, test = TRUE, impute = "avg", normMethod = "quantile", ...)
参数----------Arguments----------
参数：dataFile
csv or tab delimit file contain expression measurement that are output from AB1700 software
csv或制表符分隔文件包含表达测量AB1700软件输出
参数：designFile
Experiment design file, including information for sample type and additional phenotype information.
实验设计文件，包括样品类型和额外的表型信息的信息。
参数：group
Specify which group statistical test will be performed on. The samples will be ordered according the group.
指定哪个组统计测试将进行。根据该组的样品将被责令。
参数：test
Specify whether to perform t test. By default, t test will be performed using specified group information.
指定是否进行t检验。默认情况下，t检验将使用指定的组信息。
参数：impute
Treat flagged value (above 5000) as missing value, and impute the missing value.
视为缺失值标记值（5000以上），意指缺少的值。
参数：normMethod
The method of normalizaiton. The default is "quantile". The following normMethods are supported: quantile, mean, median, trimMean, and trimAMean. If the parameter value is one of the supported normMethods, the analysis will be performed on the chosen method. If the parameter value is "all", the analysis will be performed on quantile only, but the normalization results will be produced for each of the normMethods.
方法的normalizaiton。默认是“分量”。支持以下normMethods位数，平均数，中位数，TRIMMEAN，trimAMean。如果参数值是，支持normMethods之一，所选择的方法进行分析。如果参数值是“所有”，将进行分析，只对位数，但标准化的结果将会为每个normMethods的生产。
参数：...
Additional arguments. Use snThresh and/or detectSample to perform filtering. snThresh is the threshold of S/N value to be considered that the probe is detected (default value = 3, if snThresh is not specified). detectSample is used to determine if a probe should be included in statistical analysis (default value = 0.5, ie 50% of samples in any one subgroup).
额外的参数。使用snThresh和/或detectSample的执行过滤。 snThresh是要考虑探针检测（默认值= 3，如果snThresh未指定）的S / N值的阈值。 detectSample用于确定如果探针应包括在统计分析（默认值= 0.5，即50％的样品中的任何一个子群）。
Details
详情----------Details----------
The function works on AB1700 software export data file. It expects certain file format to work. The rows of the file represent probes. The columns should contain these headings: probeID, geneID, Signal, S/N, Flag, and optionally SDEV, CV, AssayNormSignal (these values will be ignored in the process).
该功能适用于AB1700软件出口数据文件。预计某些文件格式的工作。该文件的行代表探针。列应该包含这些标题：probeID，geneID，信号，S / N标志，并有选择地发展局局长，简历，AssayNormSignal（这些值将在这个过程中忽略）。
It is optional to have control probes. If they are present, plots will be generated for the control probes and they will be removed for further analysis.
它是可选的有控制的探针。如果它们存在，图将被控制探针产生，他们将作进一步的分析中删除。
It is required to have an experiment design file in certain format. The rows of the file are samples or arrays. The first column should be sampleName. Perhaps, sampleName should be concise and no spaces between characters. Second and third columns maybe assayName and arrayName (arrayName is optional). Additional columns should specify what type of samples. Note: It is best to have assayName the same as in dataFile.
它需要有一个实验设计在某些格式的文件。该文件的行样品或阵列。第一列应该sampleName。也许，sampleName应该是简洁和字符之间没有空格。第二和第三列可能：assayName和ARRAYNAME（ARRAYNAME是可选的）。额外的列，应指定何种类型的样品。注：这是最好的，已assayName在数据文件相同。
Group name should be the same as in designFile. The samples will be ordered according the group information. The samples within the same subgroup will be ordered together. Only one group is accepted.
组的名称应该是作为在designFile相同。根据该组信息，将被责令样品。在同一小组的样品将被责令在一起。只有一组被接受。
If test is TRUE (default), t test and ANOVA (if applicable) results will be produced.
如果测试是TRUE（默认），t检验和方差分析（如适用）的结果将产生。
If impute is avg (default), the signal values of the flagged probes will be imputed from average of the subgroup only if there are 2 or more values remaining in the subgroup.
如果归罪于是AVG（默认），标记探针的信号值将被归咎于从分组平均只有留在该小组有2个或多个值。
Even if snThresh is not specified in the argument, snThresh is set to 3 by default. If a value other than 3 is desired (e.g., 2), put 'snThresh = 2' in the argument.
即使没有参数中指定snThresh，snThresh设置为3，默认情况下。如果价值超过3所需（例如，2），把“snThresh = 2的说法。
detectSample is also preset to a value = 0.5. This means that if a probe is detected in 50% or more samples in any subgroup within the group, it is included in statistical analysis. For example, if the group is named 'tissue', and there are 2 subgroups named 'lung' and 'liver', then, if a probe is detected in 50% or more samples in 'lung', it is included in the statistical analysis regardless the detectability in the other subgroup ('liver').
detectSample也是预设的值= 0.5。这意味着，如果在50％以上的样品，在组内的任何群检测探针，它被列入统计分析。例如，如果组被命名为“组织”，并有2个亚组名为肺和肝，然后，如果在50％以上的样本，在“肺”检测探针，它包括在统计分析无论在其他分组（肝脏）的探测。
值----------Value----------
An ExpressionSet object. The assayDataElement(eset, "exprs") will be populated with normalized signals, assayDataElement(eset, "snDetect") will be populated with S/N ratio values, and the phenoData slot will be populated with information from designFile. Further analysis can be performed on the ExpressionSet object with various R and Bioconductor packages.
ExpressionSet对象。将assayDataElement(eset, "exprs")归信号，assayDataElement(eset, "snDetect")将与S / N比率值填充填充，从phenoData信息将填充designFile插槽。进一步分析，可以进行各种R和Bioconductor包ExpressionSet对象。
作者（S）----------Author(s)----------
Y Andrew Sun <sunya@appliedbiosystems.com>
参见----------See Also----------
doPlotEset, doPlotFCT, doANOVA, matrixPlot, mvaPair2, doLPE,
doPlotEset，doPlotFCT，doANOVA，matrixPlot，mvaPair2，doLPE
举例----------Examples----------
#- eset <- ABarray(dataFile, designFile, "sampleGroup")[ - ESET < - ABarray（DATAFILE，designFile“sampleGroup”）]
#- eset <- ABarray(dataFile, designFile, "group", detectSample = 0.8)[ - ESET < - ABarray（DATAFILE，designFile，“组”，detectSample = 0.8）]
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。
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发表于 2012-2-25 10:55:24
