[Qpcr-commits] r139 - in pkg/NormqPCR: data inst/doc man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Jun 30 16:41:19 CEST 2011
Author: jperkins
Date: 2011-06-30 16:41:19 +0200 (Thu, 30 Jun 2011)
New Revision: 139
Modified:
pkg/NormqPCR/data/Bladder.RData
pkg/NormqPCR/data/BladderRepro.RData
pkg/NormqPCR/data/Colon.RData
pkg/NormqPCR/data/geNorm.RData
pkg/NormqPCR/inst/doc/NormqPCR.Rnw
pkg/NormqPCR/man/Bladder.Rd
pkg/NormqPCR/man/BladderRepro.Rd
pkg/NormqPCR/man/Colon.Rd
pkg/NormqPCR/man/deltaCt.Rd
pkg/NormqPCR/man/deltaDeltaCt.Rd
pkg/NormqPCR/man/geNorm.Rd
pkg/NormqPCR/man/selectHKs.Rd
pkg/NormqPCR/man/stabMeasureM.Rd
pkg/NormqPCR/man/stabMeasureRho.Rd
Log:
changed data around so the data was in qPCRBatch form
Modified: pkg/NormqPCR/data/Bladder.RData
===================================================================
(Binary files differ)
Modified: pkg/NormqPCR/data/BladderRepro.RData
===================================================================
(Binary files differ)
Modified: pkg/NormqPCR/data/Colon.RData
===================================================================
(Binary files differ)
Modified: pkg/NormqPCR/data/geNorm.RData
===================================================================
(Binary files differ)
Modified: pkg/NormqPCR/inst/doc/NormqPCR.Rnw
===================================================================
--- pkg/NormqPCR/inst/doc/NormqPCR.Rnw 2011-06-29 22:26:15 UTC (rev 138)
+++ pkg/NormqPCR/inst/doc/NormqPCR.Rnw 2011-06-30 14:41:19 UTC (rev 139)
@@ -202,9 +202,7 @@
which is called {\it geNorm}. We first load the package and the data
<<NormqPCR>>=
options(width = 68)
-path <- system.file("exData", package = "NormqPCR")
-geNorm.example <- file.path(path, "qPCR.geNorm.txt")
-geNorm.qPCRBatch <- read.qPCR(geNorm.example)
+data(geNorm)
str(exprs(geNorm.qPCRBatch))
@
We start by ranking the selected reference/housekeeping genes. The geNorm
@@ -296,20 +294,15 @@
{\it NormFinder}.\\
The ranking contained in Table~3 of And04 can be obtained via
<<NormFinder>>=
-Colon.example <- file.path(path, "qPCR.colon.txt")
-Colon.qPCRBatch <- read.qPCR(Colon.example)
+data(Colon)
str(exprs(Colon.qPCRBatch))
-Colon.qPCRBatch[["Group"]] <- c(rep("Normal",10),rep("Dukes A",10),rep("Dukes
-B",10),rep("Dukes C",10))
pData(Colon.qPCRBatch)
res.Colon <- stabMeasureRho(Colon.qPCRBatch,
log = FALSE)
sort(res.Colon) # cf. Table 3 in Andersen et al (2004)
-Bladder.example <- file.path(path, "qPCR.bladder.txt")
-Bladder.qPCRBatch <- read.qPCR(Bladder.example)
+data(Bladder)
str(exprs(Bladder.qPCRBatch))
-Bladder.qPCRBatch[["Group"]] <- c(rep("Ta",10),rep("T1",8),rep("T2-4",10))
pData(Bladder.qPCRBatch)
res.Bladder <- stabMeasureRho(Bladder.qPCRBatch,
@@ -354,7 +347,7 @@
data:
<<taqman read dCt>>=
path <- system.file("exData", package = "NormqPCR")
-taqman.example <- paste(path, "/example.txt", sep="")
+taqman.example <- file.path(path, "example.txt")
qPCR.example <- file.path(path, "qPCR.example.txt")
qPCRBatch.taqman <- read.taqman(taqman.example)
@
@@ -407,12 +400,12 @@
data:
<<taqman read>>=
path <- system.file("exData", package = "NormqPCR")
-taqman.example <- paste(path, "/example.txt", sep="")
+taqman.example <- file.path(path, "example.txt")
qPCR.example <- file.path(path, "qPCR.example.txt")
qPCRBatch.taqman <- read.taqman(taqman.example)
@
-\code{deltaDeltaCt} and \code{deltaDeltaAvgCt} also require a contrast matrix.
+\code{deltaDeltaCt} also requires a contrast matrix.
This is to contain columns which will be used to specify the samples
representing \code{case} and \code{control} which are to be compared, in a
similar way to the \pkg{limma} package. these columns should contain 1s or 0s
Modified: pkg/NormqPCR/man/Bladder.Rd
===================================================================
--- pkg/NormqPCR/man/Bladder.Rd 2011-06-29 22:26:15 UTC (rev 138)
+++ pkg/NormqPCR/man/Bladder.Rd 2011-06-30 14:41:19 UTC (rev 139)
@@ -1,15 +1,16 @@
\name{Bladder}
\alias{Bladder}
+\alias{Bladder.qPCRBatch}
\docType{data}
\title{ Data set of Andersen et al (2004) }
\description{
This data set was used in Andersen et al (2004) to demonstrate normalization
of real-time quantitative RT-PCR data by geometric averaging of housekeeping genes.
}
-\usage{data(geNorm)}
+\usage{data(Bladder)}
\format{
- A data frame with 28 observations on the following 16 variables which stand for
- expression data of 14 potential reference/housekeeping genes
+ A qPCRBatch object which contains an expression matrix with 28 observations on the following 14 variables which stand for
+ expression data potential reference/housekeeping genes
\describe{
\item{\code{Grade}}{Grade of bladder cancer. }
\item{\code{Sample.no.}}{sample number. }
@@ -28,6 +29,8 @@
\item{\code{UBC}}{Ubiquitin C. }
\item{\code{FLJ20030}}{Hypothetical protein FLJ20030. }
}
+ It also contains a "group" column in the pData slot, which gives information on the different sample classes,
+ necessary for the NormFinder algorithm
}
\details{
The genes included in this data set were selected by screening 99 bladder
@@ -46,7 +49,8 @@
\url{http://cancerres.aacrjournals.org/cgi/content/full/64/15/5245}
}
\examples{
-data(Bladder)
-str(Bladder)
+ data(Bladder)
+ head(exprs(Bladder.qPCRBatch))
+ pData(Bladder.qPCRBatch)
}
\keyword{datasets}
Modified: pkg/NormqPCR/man/BladderRepro.Rd
===================================================================
--- pkg/NormqPCR/man/BladderRepro.Rd 2011-06-29 22:26:15 UTC (rev 138)
+++ pkg/NormqPCR/man/BladderRepro.Rd 2011-06-30 14:41:19 UTC (rev 139)
@@ -1,15 +1,16 @@
\name{BladderRepro}
\alias{BladderRepro}
+\alias{BladderRepro.qPCRBatch}
\docType{data}
\title{ Data set of Andersen et al (2004) }
\description{
This data set was used in Andersen et al (2004) to demonstrate normalization
of real-time quantitative RT-PCR data by geometric averaging of housekeeping genes.
}
-\usage{data(geNorm)}
+\usage{data(BladderRepro)}
\format{
- A data frame with 26 observations on the following 10 variables which stand for
- expression data of the following genes
+ A qPCRBatch object which contains an expression matrix with 28 observations on the following 14 variables which stand for
+ expression data potential reference/housekeeping genes
\describe{
\item{\code{Grade}}{Grade of bladder cancer. }
\item{\code{Sample.no.}}{sample number. }
@@ -22,6 +23,8 @@
\item{\code{ACTB}}{Actin, beta. }
\item{\code{GAPD}}{Glyceraldehyde-3-phosphate dehydrogenase. }
}
+ It also contains a "group" column in the pData slot, which gives information on the different sample classes,
+ necessary for the NormFinder algorithm
}
\details{
This data set was used to check the reproducibility of the results obtained
@@ -40,7 +43,8 @@
\url{http://cancerres.aacrjournals.org/cgi/content/full/64/15/5245}
}
\examples{
-data(Bladder)
-str(Bladder)
+ data(BladderRepro)
+ head(exprs(BladderRepro.qPCRBatch))
+ pData(BladderRepro.qPCRBatch)
}
\keyword{datasets}
Modified: pkg/NormqPCR/man/Colon.Rd
===================================================================
--- pkg/NormqPCR/man/Colon.Rd 2011-06-29 22:26:15 UTC (rev 138)
+++ pkg/NormqPCR/man/Colon.Rd 2011-06-30 14:41:19 UTC (rev 139)
@@ -1,18 +1,16 @@
\name{Colon}
\alias{Colon}
+\alias{Colon.qPCRBatch}
\docType{data}
\title{ Data set of Andersen et al (2004) }
\description{
This data set was used in Andersen et al (2004) to demonstrate normalization
of real-time quantitative RT-PCR data by geometric averaging of housekeeping genes.
}
-\usage{data(geNorm)}
+\usage{data(Colon)}
\format{
- A data frame with 40 observations on the following 15 variables which stand for
- expression data of 13 potential reference/housekeeping genes
+ A qPCRBatch object which contains an expression matrix with 40 observations on the following 13 variables
\describe{
- \item{\code{Classification}}{Colon cancer classification. }
- \item{\code{Sample.no.}}{sample number. }
\item{\code{UBC}}{Ubiquitin C. }
\item{\code{UBB}}{Ubiquitin B. }
\item{\code{SUI1}}{Putative translation initiation factor. }
@@ -27,6 +25,8 @@
\item{\code{TPT1}}{Tumor protein, translationally controlled 1. }
\item{\code{TUBA6}}{Tubulin alpha 6. }
}
+ It also contains a "group" column in the pData slot, which gives information on the different sample classes,
+ necessary for the NormFinder algorithm
}
\details{
The genes included in this data set were selected by screening 161 colon
@@ -45,7 +45,8 @@
\url{http://cancerres.aacrjournals.org/cgi/content/full/64/15/5245}
}
\examples{
-data(Colon)
-str(Colon)
+ data(Colon)
+ head(exprs(Colon.qPCRBatch))
+ pData(Colon.qPCRBatch)
}
\keyword{datasets}
Modified: pkg/NormqPCR/man/deltaCt.Rd
===================================================================
--- pkg/NormqPCR/man/deltaCt.Rd 2011-06-29 22:26:15 UTC (rev 138)
+++ pkg/NormqPCR/man/deltaCt.Rd 2011-06-30 14:41:19 UTC (rev 139)
@@ -12,7 +12,7 @@
\S4method{deltaCt}{qPCRBatch}(qPCRBatch, hkgs, combineHkgs=FALSE, calc="arith")
}
\arguments{
- \item{qPCRBatch}{ Expression set containing qPCR data. }
+ \item{qPCRBatch}{ qPCR-specific expression set, containing qPCR data. }
\item{\dots}{ Extra arguments, detailed below }
\item{hkgs}{ String containing the name of the name of the housekeeping gene which will be used to normalise the rest of the genes.}
\item{combineHkgs}{ Logical - if TRUE, then as long as more than one housekeeper given for argument hkgs, it will combine the housekeepers by finding the geometric mean. Housekeepers can be found using geNorm or NormFinder algorithms.}
@@ -25,10 +25,21 @@
qPCRBatch with exprs set of the same dimensions but with the given hkg value subtracted.
}
-%\references{ }
+\references{
+ Schmittgen TD, Livak KJ (2008)
+ Analyzing real-time PCR data by the comparative C(T) method.
+ NATURE PROTOCOLS. 3(6):1101-8
+ \url{http://www.nature.com/nprot/journal/v3/n6/full/nprot.2008.73.html}
+}
\author{ James Perkins \email{jperkins at biochem.ucl.ac.uk}}
%\note{}
-%\seealso{}
-%\examples{
-%}
+\seealso{\code{selectHKs}, \code{deltaDeltaCt}}
+\examples{
+ path <- system.file("exData", package = "NormqPCR")
+ taqman.example <- file.path(path, "example.txt")
+ qPCRBatch.taqman <- read.taqman(taqman.example)
+ hkgs<-"Actb-Rn00667869_m1"
+ qPCRBatch.norm <- deltaCt(qPCRBatch = qPCRBatch.taqman, hkgs = hkgs, calc="arith")
+ head(exprs(qPCRBatch.norm))
+}
\keyword{data}
Modified: pkg/NormqPCR/man/deltaDeltaCt.Rd
===================================================================
--- pkg/NormqPCR/man/deltaDeltaCt.Rd 2011-06-29 22:26:15 UTC (rev 138)
+++ pkg/NormqPCR/man/deltaDeltaCt.Rd 2011-06-30 14:41:19 UTC (rev 139)
@@ -15,7 +15,7 @@
case, control, paired=TRUE, hkgCalc="arith", statCalc="arith")
}
\arguments{
- \item{qPCRBatch}{ Expression set containing qPCR data. }
+ \item{qPCRBatch}{ qPCR-specific expression set, containing qPCR data. }
\item{\dots}{ Extra arguments, detailed below }
\item{maxNACase}{ Maximum number of NA values allowed before a detector's reading is discarded for samples designated as case. }
\item{maxNAControl}{ Maximum number of NA values allowed before a detector's reading is discarded for samples designated as control. }
@@ -33,10 +33,26 @@
\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 )
}
-%\references{ }
+\references{
+ Schmittgen TD, Livak KJ (2008)
+ Analyzing real-time PCR data by the comparative C(T) method.
+ NATURE PROTOCOLS. 3(6):1101-8
+ \url{http://www.nature.com/nprot/journal/v3/n6/full/nprot.2008.73.html}
+}
\author{ James Perkins \email{jperkins at biochem.ucl.ac.uk}}
%\note{}
-%\seealso{}
-%\examples{
-%}
+\seealso{\code{selectHKs}, \code{deltaCt}}
+\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)
+}
\keyword{data}
Modified: pkg/NormqPCR/man/geNorm.Rd
===================================================================
--- pkg/NormqPCR/man/geNorm.Rd 2011-06-29 22:26:15 UTC (rev 138)
+++ pkg/NormqPCR/man/geNorm.Rd 2011-06-30 14:41:19 UTC (rev 139)
@@ -1,5 +1,6 @@
\name{geNorm}
\alias{geNorm}
+\alias{geNorm.qPCRBatch}
\docType{data}
\title{ Data set of Vandesompele et al (2002) }
\description{
@@ -8,7 +9,7 @@
}
\usage{data(geNorm)}
\format{
- A data frame with 85 observations on the following 10 variables which stand for
+ A qPCRBatch object which contains an expression matrix with 85 observations on the following 10 variables which stand for
expression data of ten potential reference/housekeeping genes
\describe{
\item{\code{ACTB}}{actin, beta}
@@ -47,8 +48,8 @@
\url{http://genomebiology.com/2002/3/7/research/0034/}
}
\examples{
-data(geNorm)
-str(geNorm)
-rownames(geNorm)
+ data(geNorm)
+ str(exprs(geNorm.qPCRBatch))
+ sampleNames(geNorm.qPCRBatch)
}
\keyword{datasets}
Modified: pkg/NormqPCR/man/selectHKs.Rd
===================================================================
--- pkg/NormqPCR/man/selectHKs.Rd 2011-06-29 22:26:15 UTC (rev 138)
+++ pkg/NormqPCR/man/selectHKs.Rd 2011-06-30 14:41:19 UTC (rev 139)
@@ -14,7 +14,7 @@
trace = TRUE, na.rm = TRUE)
}
\arguments{
- \item{qPCRBatch}{ qPCRBatch, containing the data }
+ \item{qPCRBatch}{ qPCRBatch, containing the data (expression matrix) in the exprs slot }
\item{\dots}{ Extra arguments, detailed below }
\item{group}{ optional factor not used by all methods, hence may be missing }
\item{method}{ method to compute most stable genes }
@@ -72,12 +72,10 @@
%}
%\seealso{}
\examples{
-path <- system.file("exData", package = "NormqPCR")
-geNorm.example <- file.path(path, "qPCR.geNorm.txt")
-geNorm.qPCRBatch <- read.qPCR(geNorm.example)
-tissue <- as.factor(c(rep("BM", 9), rep("FIB", 20), rep("LEU", 13),
- rep("NB", 34), rep("POOL", 9)))
-res.BM <- selectHKs(geNorm.qPCRBatch[,tissue == "BM"], method = "geNorm",
- Symbols = featureNames(geNorm.qPCRBatch), minNrHK = 2, log = FALSE)
+ data(geNorm)
+ tissue <- as.factor(c(rep("BM", 9), rep("FIB", 20), rep("LEU", 13),
+ rep("NB", 34), rep("POOL", 9)))
+ res.BM <- selectHKs(geNorm.qPCRBatch[,tissue == "BM"], method = "geNorm",
+ Symbols = featureNames(geNorm.qPCRBatch), minNrHK = 2, log = FALSE)
}
\keyword{data}
Modified: pkg/NormqPCR/man/stabMeasureM.Rd
===================================================================
--- pkg/NormqPCR/man/stabMeasureM.Rd 2011-06-29 22:26:15 UTC (rev 138)
+++ pkg/NormqPCR/man/stabMeasureM.Rd 2011-06-30 14:41:19 UTC (rev 139)
@@ -38,7 +38,10 @@
%}
\seealso{\code{selectHKs}}
\examples{
-data(geNorm)
-res.BM <- stabMeasureM(geNorm[1:9,], log = FALSE)
+ data(geNorm)
+ tissue <- as.factor(c(rep("BM", 9), rep("FIB", 20), rep("LEU", 13),
+ rep("NB", 34), rep("POOL", 9)))
+ res.BM <- selectHKs(geNorm.qPCRBatch[,tissue == "BM"], method = "geNorm",
+ Symbols = featureNames(geNorm.qPCRBatch), minNrHK = 2, log = FALSE)
}
\keyword{data}
Modified: pkg/NormqPCR/man/stabMeasureRho.Rd
===================================================================
--- pkg/NormqPCR/man/stabMeasureRho.Rd 2011-06-29 22:26:15 UTC (rev 138)
+++ pkg/NormqPCR/man/stabMeasureRho.Rd 2011-06-30 14:41:19 UTC (rev 139)
@@ -45,14 +45,14 @@
%}
\seealso{\code{selectHKs}}
\examples{
-data(Colon.qPCRBatch)
-Colon.qPCRBatch[["Group"]] <- c(rep("Normal",10),rep("Dukes A",10),rep("Dukes B",10),rep("Dukes C",10))
-res.Colon <- stabMeasureRho(Colon.qPCRBatch,
+ data(Colon.qPCRBatch)
+ Colon.qPCRBatch[["Group"]] <- c(rep("Normal",10),rep("Dukes A",10),rep("Dukes B",10),rep("Dukes C",10))
+ res.Colon <- stabMeasureRho(Colon.qPCRBatch,
log = FALSE)
-sort(res.Colon) # cf. Table 3 in Andersen et al (2004)
-data(Bladder.qPCRBatch)
-res.Bladder <- stabMeasureRho(Bladder.qPCRBatch,
+ sort(res.Colon) # cf. Table 3 in Andersen et al (2004)
+ data(Bladder.qPCRBatch)
+ res.Bladder <- stabMeasureRho(Bladder.qPCRBatch,
log = FALSE)
-sort(res.Bladder) # cf. Table 3 in Andersen et al (2004)
+ sort(res.Bladder) # cf. Table 3 in Andersen et al (2004)
}
\keyword{data}
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