R语言 Ringo包 preprocess()函数中文帮助文档(中英文对照)

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preprocess(Ringo)
preprocess()所属R语言包：Ringo

                                        Preprocess Raw ChIP-chip Intensities
                                         预处理原始芯片的芯片强度

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

Calls one of various (limma) functions to transform raw probe intensities into (background-corrected) normalized log ratios (M-values).
调用一个不同（limma）函数来转换原始探针强度（背景校正）归log比（m值）。


用法----------Usage----------


preprocess(myRG, method="vsn", ChIPChannel="R", inputChannel="G",
           returnMAList=FALSE, idColumn="PROBE_ID", verbose=TRUE, ...)



参数----------Arguments----------

参数：myRG
object of class RGList
对象类RGList


参数：method
string; denoting which normalization method to choose, see below for details
字符串;汉语表，其中规范化的方法来选择，请参阅以下详细


参数：ChIPChannel
string; which element of the RGList holds the  ChIP result, see details
字符串;RGList持有芯片的结果，看到的元素的详细信息


参数：inputChannel
string; which element of the RGList holds the  untreated input sample; see details
字符串;元素RGList持有未处理的输入样本;查看详细信息


参数：returnMAList
logical; should an MAList object be returned? Default is to return an ExpressionSet object.
逻辑;应MAList对象返回？默认返回ExpressionSet对象。


参数：idColumn
string; indicating which column of the genes data.frame of the RGList holds the identifier for reporters on the microarray. This column, after calling make.names on it, will make up the unique featureNames of the resulting ExpressionSet. If argument returnMAList is TRUE, this argument is ignored.
字符串;genesRGList的数据框列持有记者芯片的标识符。此列，后调用make.names就可以了，将弥补由此产生的featureNames独特ExpressionSet。如果参数returnMAList是TRUE，这种说法被忽略。


参数：verbose
logical; progress output to STDOUT?
逻辑;输出到STDOUT进展？


参数：...
further arguments to be passed on normalizeWithinArrays and normalizeBetweenArrays
normalizeWithinArrays和normalizeBetweenArrays通过进一步的参数


Details

详情----------Details----------

The procedure and called limma functions depend on the choice of method.
程序和一个名为limma功能取决于方法的选择。




loess Calls normalizeWithinArrays with
黄土呼唤normalizeWithinArrays




vsn Calls normalizeBetweenArrays with
VSN呼唤normalizeBetweenArrays




Gquantile Calls normalizeBetweenArrays with
normalizeBetweenArraysgquantile呼吁




Rquantile Calls normalizeBetweenArrays with
normalizeBetweenArraysrquantile呼吁




median Calls normalizeWithinArrays with
位数检测normalizeWithinArrays




nimblegen Scaling procedure used by Nimblegen. Yields scaled log-ratios by a two step procedure: srat = log2(R) - log2(G)
NimbleGen的缩放过程中使用的NimbleGen。产量缩减log比率由两个步骤：SRAT =为log2（R）的 - 为log2（Ğ）




Gvsn Learns vsn model on green channel intensities only and applies that transformation to both channels before
gvsn学习绿色通道强度vsn模型，并应用于两个通道前，改造




Rvsn Learns vsn model on red channel intensities only and applies that transformation to both channels before
RVSN学习强度只有红色通道vsn模型，并应用于两个通道前，改造




none No normalization of probe intensities, takes raw log2(R)-log2(G) as component M and (log2(R)+log2(G))/2 as component A;
无探针强度的标准化，需要原料log2(R)-log2(G)作为组件M和(log2(R)+log2(G))/2作为组件A;

Mostly with two-color ChIP-chip, the ChIP sample is marked with the red Cy5 dye and for the untreated input sample the green Cy3 dye is used. In that case the RGListmyRG's element R holds the ChIP data, and element G holds the input data. If this is not the case with your data, use the  arguments ChIPChannel and inputChannel to specify the respective elements of myRG.
大多是两色芯片的芯片，该芯片的样品被标记为红色的Cy5染料和未处理的输入样本的绿色Cy3染料用于。在这种情况下，RGList myRG的元素R持有芯片的数据，元素G持有的输入数据。如果这是不是与您的数据的情况下，使用参数ChIPChannel和inputChannel指定myRG的相应元素。


值----------Value----------

Returns normalized, transformed values as an object of class ExpressionList or MAList.
返回规范化，转换后的值作为一个对象类ExpressionList或MAList。


注意----------Note----------

Since Ringo version 1.5.6, this function does not call limma's function backgroundCorrect directly any longer. If wanted by the user, background correction should be indicated as additional arguments passed on to normalizeWithinArrays or normalizeBetweenArrays, or alternatively call  backgroundCorrect on the RGList before preprocessing.
由于林檎版本1.5.6，这个函数不调用limma的功能backgroundCorrect直接不再。如果用户想应该指出，背景校正为附加参数传递normalizeWithinArrays或normalizeBetweenArrays，或者叫backgroundCorrectRGList的前preprocess ING。


作者（S）----------Author(s)----------


Joern Toedling



参见----------See Also----------

normalizeWithinArrays, normalizeBetweenArrays, malist, ExpressionSet,   
normalizeWithinArrays，normalizeBetweenArrays，malist，ExpressionSet


举例----------Examples----------


   exDir <- system.file("exData",package="Ringo")
   exRG <- readNimblegen("example_targets.txt","spottypes.txt",
                         path=exDir)
   exampleX <- preprocess(exRG)
   sampleNames(exampleX) <- make.names(paste(exRG$targets$Cy5,"vs",
                                        exRG$targets$Cy3,sep="_"))
   print(exampleX)
   ### compare VSN to NimbleGen's tukey-biweight scaling[＃比较的VSN NimbleGen的杜克biweight缩放]
   exampleX.NG <- preprocess(exRG, method="nimblegen")
   sampleNames(exampleX.NG) <- sampleNames(exampleX)
   if (interactive())
     corPlot(cbind(exprs(exampleX),exprs(exampleX.NG)),
       grouping=c("VSN normalized","Tukey-biweight scaled"))

转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。


注：
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