deltaDeltaCt(NormqPCR)
deltaDeltaCt()所属R语言包：NormqPCR
Perform normalization and differential expression with given housekeeping gene
执行给定的看家基因差异表达的标准化
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Normalise qPCR eset using housekeeping genes as control, then perform differential expression analysis using the delta delta Ct method. Differs from the deltaDeltaAvgCt method in that the hkg values are subtracted and the sd is calculated on the differences (i.e. paired). Suitable when housekeeping genes are from same wells/sample as the other detectors
Normalise qPCR的的ESET使用看家基因作为控制，然后进行差异表达分析DeltaDeltaCT方法。不同于方法HKG值减去计算上的差异（即配对）和SD的deltaDeltaAvgCt。适合当管家基因是从同一井/样品作为其他探测器
用法----------Usage----------
deltaDeltaCt(qPCRBatch,...)
## S4 method for signature 'qPCRBatch'
deltaDeltaCt(qPCRBatch, maxNACase=0, maxNAControl=0, hkgs, contrastM,
case, control, paired=TRUE, hkgCalc="arith", statCalc="arith")
参数----------Arguments----------
参数：qPCRBatch
qPCR-specific expression set, containing qPCR data.
定量PCR特异性表达的集合，包含qPCR数据。
参数：...
Extra arguments, detailed below
额外的参数，下面详细介绍
参数：maxNACase
Maximum number of NA values allowed before a detector's reading is discarded for samples designated as case.
前探测器的读数允许NA值的最大数量的指定作为情况的样本将被丢弃。
参数：maxNAControl
Maximum number of NA values allowed before a detector's reading is discarded for samples designated as control.
前一个探测器的读数允许NA值的最大数量将被丢弃指定作为对照样本。
参数：hkgs
String containing the name of th name of the housekeeping gene which will be used to normalise the rest of the genes.
字符串含有届看家基因的名称，将用于标准化其余的基因的名称。
参数：contrastM
A binary matrix which designates case and control samples.
二进制矩阵指定病例和对照样本。
参数：case
The name of the column in contrastM that corresponds to the case samples.
的在contrastM列对应的情况下样品的名称。
参数：control
The name of the column in contrastM that corresponds to the control samples.
列对应的控制样品在contrastM的名称。
参数：paired
Logical - if TRUE the detectors and housekeepers in the same sample will be paired for calculating standard deviation, effectively meaning we will be calculating standard deviation of the differences. If FALSE, there will be no pairing, and standard deviation will be pooled between the detector and housekeepers.
逻辑 - 如果为TRUE，将在同一样品的探测器和管家配对计算标准偏差，有效地意味着我们将计算标准偏差的差异。如果为false，将没有配对，将汇集与探测器之间的管家和标准偏差。
参数：hkgCalc
String - either "arith" or "geom", details how the different housekeeper genes should be combined - either by using the arithmetic or geometric mean.
字符串 - 或者“arith”或“GEOM”，详细介绍了如何在不同的管家基因，应结合 - 通过使用算术或几何平均数。
参数：statCalc
String - either "arith" or "geom", details how genes should be combined - either by using the arithmetic or geometric mean.
字符串 - 或者“arith”或“GEOM”，详情如何，应结合基因 - 通过使用算术或几何平均数。
Details
详情----------Details----------
Takes expression set of qPCR values and normalises them using different housekeeping genes. Returns seperate sets of values for each housekeeping gene given.
需要表达的qPCR值设置和使用不同的看家基因normalises他们。返回逗号分开给每个看家基因组值。
值----------Value----------
matrix with columns containing the detector ids, 2^delta Ct values for the sample of interest and the callibrator sample, alongside their respective standard deviations, the 2^delta delta Ct values and the minimum and maximum values (ie the values that are 1 sd away )
含探测器IDS，2 ^Delta利益和callibrator样品样本的CT值，沿着各自的标准偏差，2列的矩阵，^DeltaDelta的CT值和最低和最高值（即值是1个SD距离）
作者（S）----------Author(s)----------
James Perkins <a href="mailto:jperkins@biochem.ucl.ac.uk">jperkins@biochem.ucl.ac.uk</a>
参考文献----------References----------
Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2^DDCt Method. Methods 25, 402-408, 2001 http://www.ncbi.nlm.nih.gov/pubmed/11846609
参见----------See Also----------
selectHKs, deltaCt
selectHKs，deltaCt
举例----------Examples----------
path <- system.file("exData", package = "NormqPCR")
taqman.example <- file.path(path, "example.txt")
qPCRBatch.taqman <- read.taqman(taqman.example)
hkg <- "Actb-Rn00667869_m1"
contM <- cbind(c(0,0,1,1,0,0,1,1),c(1,1,0,0,1,1,0,0))
colnames(contM) <- c("interestingPhenotype","wildTypePhenotype")
rownames(contM) <- sampleNames(qPCRBatch.taqman)
ddCt.taqman <- deltaDeltaCt(qPCRBatch = qPCRBatch.taqman, maxNACase=1, maxNAControl=1, hkg=hkg, contrastM=contM, case="interestingPhenotype", control="wildTypePhenotype", statCalc="geom", hkgCalc="arith")
head(ddCt.taqman)
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。
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发表于 2012-2-26 07:51:05
