compareLimmapumaDE(puma)
compareLimmapumaDE()所属R语言包：puma
Compare pumaDE with a default Limma model
与默认Limma模型比较pumaDE
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This function compares the identification of differentially expressed (DE) genes using the pumaDE function and the limma package.
这个功能比较鉴定差异表达的基因（DE）的使用pumaDE函数和limma包。
用法----------Usage----------
compareLimmapumaDE(
eset_mmgmos
, eset_comb = NULL
, eset_other = eset_mmgmos
, limmaRes = calculateLimma(eset_other)
, pumaDERes = pumaDE(eset_comb)
, contrastMatrix = createContrastMatrix(eset_mmgmos)
, numberToCompareForContrasts = 3
, numberToCompareForVenn = 100
, plotContrasts = TRUE
, contrastsFilename = NULL
, plotOther = FALSE
, otherFilename = "other"
, plotBcombContrasts = FALSE
, bcombContrastsFilename = "bcomb_contrasts"
, plotVenn = FALSE
, vennFilename = "venn.pdf"
, showTopMatches = FALSE
, returnResults = FALSE
)
参数----------Arguments----------
参数：eset_mmgmos
An object of class ExpressionSet, that includes both expression levels as well as standard errors of the expression levels. This will often have been created using mmgmos, but might also have been created by mgmos, or any other method capable of providing standard errors.
一个类的对象ExpressionSet，包括表达水平以及表达水平的标准误差。这往往会被创建使用mmgmos，但也可能已经mgmos，或任何其他的方法能够提供标准的错误。
参数：eset_comb
An object of class ExpressionSet, includes both expression levels as well as standard errors of the expression levels for each unique condition in an experiment (i.e. created from combining the information from each replicate). This will usually have been created using pumaComb.
一个类的对象ExpressionSet，包括表达水平以及表达水平的标准误差在实验中，为每一个独特的条件（即创建相结合的信息，从每个重复）。这通常会使用pumaComb已创建。
参数：eset_other
An object of class ExpressionSet, that includes expression levels , and may optionally also include standard errors of the expression levels. This is used for comparison with eset_mmgmos, and might have been created by any summarisation method, e.g. rma.
ExpressionSet类的对象，其中包括表达水平，可以选择还包括表达水平的标准误差。这是用于比较eset_mmgmos，并可能已被创建任何方法summarisation，例如rma。
参数：limmaRes
A list with two elements, usually created using the function calculateLimma. The first element is a matrix of p-values. Each column represent one contrast. Within each column the p-values are ordered. The second element is a matrix of row numbers, which can be used to map p-values back to probe sets. If not supplied this will be automatically created from eset_other.
一个有两个元素的列表，通常使用功能calculateLimma。第一个元素是一个p-值的矩阵。每一列代表一个对比。在每一列的p值是有序的。第二个元素是一个矩阵的行数，可用于图p值回探针集。如果没有提供，这将自动创建eset_other。
参数：pumaDERes
A list with two elements, usually created using the function pumaDE. The first element is a matrix of PPLR values. Each column represent one contrast. Within each column the PPLR values are ordered. The second element is a matrix of row numbers, which can be used to map PPLR values back to probe sets. If not supplied this will be automatically created from eset_comb.
一个有两个元素的列表，通常使用功能pumaDE。第一个元素是一个PPLR值的矩阵。每一列代表一个对比。在每一列PPLR值是有序的。第二个元素是矩阵的行数，它可以用来映射PPLR值回探针组。如果没有提供，这将自动创建eset_comb。
参数：contrastMatrix
A contrast matrix. If not supplied this will be created from eset_mmgmos
对比矩阵。如果不提供，这将创建从eset_mmgmos
参数：numberToCompareForContrasts
An integer specifying the number of most differentially expressed probe sets (genes) that will be used in comparison charts.
一个整数，指定最差异表达探针组（基因），将在比较图表。
参数：numberToCompareForVenn
An integer specifying the number of most differentially expressed probe sets (genes) that will be used for comparison in the Venn diagram.
一个整数，指定最差异表达探针组（基因），将用于在维恩图比较。
参数：plotContrasts
A boolean specifying whether or not to plot the most differentially expressed probe sets (genes) for each contrast for the eset_mmgmos ExpressionSet.
一个布尔值，指明是否绘制每个eset_mmgmosExpressionSet对比差异表达的探针组（基因）。
参数：contrastsFilename
A character string specifying a file name stem for the PDF files which will be created to hold the contrast plots for the eset_mmgmos ExpressionSet. The actually filenames will have the name of the contrast appended to this stem.
一个字符串，指定将创建的举行eset_mmgmosExpressionSet的对比图的PDF文件的文件名干。实际文件名，将名称附加到该干的对比。
参数：plotOther
A boolean specifying whether or not to plot the most differentially expressed probe sets (genes) for each contrast for the eset_other ExpressionSet.
一个布尔值，指明是否绘制每个eset_otherExpressionSet对比差异表达的探针组（基因）。
参数：otherFilename
A character string specifying a file name stem for the PDF files which will be created to hold the contrast plots for the eset_other ExpressionSet. The actually filenames will have the name of the contrast appended to this stem.
一个字符串，指定将创建的举行eset_otherExpressionSet的对比图的PDF文件的文件名干。实际文件名，将名称附加到该干的对比。
参数：plotBcombContrasts
A boolean specifying whether or not to plot the most differentially expressed probe sets (genes) for each contrast for the eset_comb ExpressionSet.
一个布尔值，指明是否绘制每个eset_combExpressionSet对比差异表达的探针组（基因）。
参数：bcombContrastsFilename
A character string specifying a file name stem for the PDF files which will be created to hold the contrast plots for the eset_comb ExpressionSet. The actually filenames will have the name of the contrast appended to this stem.
一个字符串，指定将创建的举行eset_combExpressionSet的对比图的PDF文件的文件名干。实际文件名，将名称附加到该干的对比。
参数：plotVenn
A boolean specifying whether or not to plot a Venn diagram showing the overlap in the most differentially expressed probe sets (genes) as identified from the two different methods being compared.
一个布尔值，指定是否要绘制维恩图中差异表达的探针组重叠（基因）作为被比较的两种不同的方法确定。
参数：vennFilename
A character string specifying the filename for the PDF file which will hold the Venn diagram showing the overlap in the most differentially expressed probe sets (genes) as identified from the two different methods being compared.
一个字符串，指定文件名的PDF文件，将持有的维恩图中差异表达的探针组的重叠（基因）被比较了两种不同的方法确定。
参数：showTopMatches
A boolean specifying whether or not to show the probe sets which are deemed most likely to be differentially expressed.
一个布尔值，指定是否显示探针集被视为最有可能的差异表达。
参数：returnResults
A boolean specifying whether or not to return a list containing results generated.
一个布尔值，指明是否返回一个列表，其中包含结果产生。
值----------Value----------
The main outputs from this function are a number of PDF files.
从这个函数的主要输出是一个PDF文件的数量。
The function only returns results if returnResults=TRUE
函数只返回结果，如果returnResults = TRUE，
作者（S）----------Author(s)----------
Richard D. Pearson
参见----------See Also----------
Related methods pumaDE and calculateLimma
相关方法pumaDE和calculateLimma
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 11:32:50
