SODEGIR_GEstatistics(PREDA)
SODEGIR_GEstatistics()所属R语言包：PREDA
Wrapper function for gene expression statistics preprocessing for SODEGIR analysis
包装功能基因表达的统计预处理SODEGIR分析
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Wrapper function for gene expression statistics preprocessing for SODEGIR analysis.
包装功能基因表达统计SODEGIR分析的预处理。
用法----------Usage----------
# SODEGIR_GEstatistics(.Object, pData_classColumn=NULL,
# referenceGroupLabel=NULL,
# statisticType=c("tstatistic", "FC", "FCmedian", "eBayes", "SAM"),
# singleSampleOutput=TRUE, varianceAll=FALSE)
SODEGIR_GEstatistics(.Object, ...)
参数----------Arguments----------
参数：.Object
An object of class ExpressionSet containing gene expression input data
一个类ExpressionSet的对象包含基因表达的输入数据
参数：...
See below
见下文
pData_classColumn: Column of phenoData slot from the ExpressionSet object, containing the label of sample classes
pData_classColumn：栏phenoData插槽从ExpressionSet对象，包含样本类的标签
referenceGroupLabel: Specify which class label is used for the reference sample used in computing statistics for differential expression.
referenceGroupLabel：指定用于计算统计差异表达的参考样本的类标签。
statisticType: Stastistic for differential expression that is computed on input data. Possible values are "tstatistic", "SAM" (SAM statistical score for differential expression), "FC" (Fold Change), "FCmedian" (fold change computed on medians)
statisticType：Stastistic输入数据计算的差异表达。可能的值是“tstatistic”，“萨姆”（SAM差异表达的统计得分），“财委会”（倍数更改），“FCmedian”（中位数计算倍数变化）
singleSampleOutput: Logical, if TRUE a statistic comparing each sample with the reference group is computed.
singleSampleOutput：逻辑，如果每个样品与参照组比较TRUE统计计算。
varianceAll: This parameter affect the computation only when singleSampleOutput is TRUE. varianceAll is itself a logical parameter. If TRUE, all pathological (e.g. tumor) samples and all normal (reference) samples are used to estimate variance in the comparison of individual pathological samples to the normal reference, as described in the original SODEGIR apper by Bicciato et al. (Nucleic Acids Res. 2009). The original SODEGIR statistic for Gene Expression was based on the SAM score. Therefore in the current PREDA version the varianceAll=TRUE parameter can be used only for SAM statistic: when singleSampleOutput is TRUE and a different statisticType is used, the variance is actually computed using only the normal (reference) samples. If FALSE (default value), the computation of statistics for single sample VS reference comparisons only take into account the variance in the reference group of samples.
varianceAll：此参数影响的计算，只有当singleSampleOutput为TRUE。 varianceAll本身就是一个逻辑参数。如果是TRUE，所有病变（如肿瘤）的样品和一切正常（参考）样本方差估计在个别的病理标本比较正常的参考，在的原始SODEGIR冲击片雷管描述由Bicciato等。 （核酸氨基酸水库2009年）。基因表达的原始SODEGIR统计是基于SAM的评分。因此，在当前普雷达版本的varianceAll = true参数，可以只用萨姆统计：为TRUE时singleSampleOutput，和使用不同statisticType，方差计算使用正常（参考）样本。如果为FALSE（默认值），单一样本VS参考比较的统计数据的计算只考虑在参考样本组的差异。
Details
详情----------Details----------
Using an ExpressionSet object as input, statistics for differential expression are computed comparing each sample with the reference group.
作为的输入ExpressionSet对象，计算每个样品与参照组比较差异表达的统计数字。
值----------Value----------
The output is returned as a matrix.
返回矩阵输出。
作者（S）----------Author(s)----------
Francesco Ferrari
参考文献----------References----------
Mangano, Francesco Ferrari, Luca Beltrame, Ingrid Cifola, Clelia Peano, Aldo Solari, and Cristina Battaglia. A computational procedure to identify significant overlap of differentially expressed and genomic imbalanced regions in cancer datasets. Nucleic Acids Res, 37(15):5057-70, August 2009.
参见----------See Also----------
preprocessingGE, SODEGIRpreprocessingGE, ExpressionSet
preprocessingGE，SODEGIRpreprocessingGE，ExpressionSet
转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。
注：
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发表于 2012-2-26 11:26:03
