marray: Exploratory analysis for two-color spotted microarray data
Version 1.54.0

Class definitions for two-color spotted microarray data. Fuctions for data input, diagnostic plots, normalization and quality checking.

AuthorYee Hwa (Jean) Yang <jeany@maths.usyd.edu.au> with contributions from Agnes Paquet and Sandrine Dudoit.
Bioconductor views Microarray Preprocessing TwoChannel
Date of publicationNone
MaintainerYee Hwa (Jean) Yang <jean@biostat.ucsf.edu>
LicenseLGPL
Version1.54.0
URL http://www.maths.usyd.edu.au/u/jeany/
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("marray")

Popular man pages

maColorBar: Calibration bar for color images
maMed: Stratified median calculation
mapGeneInfo: Creating URL strings for external database links
maPlot: Scatter-plots for cDNA microarray spot statistics
marrayInfo-class: Class "marrayInfo", description of target samples or spotted...
print-methods: Printing summary methods for microarray objects
swirl: Gene expression data from Swirl zebrafish cDNA microarray...
See all...

All man pages Function index File listing

Man pages

boxplot: Boxplots for cDNA microarray spot statistics
bracketMethods: Subsetting methods for microarray objects
cbind: Combine marrayRaw, marrayNorm or marrayInfo Objects
checkTargetInfo: Verifying the order between intensities matrix and target...
coerce-methods: Coerce an object to belong to a given microarray class
dim: Retrieve the Dimensions of an marrayRaw, marrayNorm or...
findID: Find ID when given an accession number
htmlPage: Display gene list as a HTML page
image: Color image for cDNA microarray spot statistics
ma2D: Stratified bivariate robust local regression
maBoxplot: Boxplots for cDNA microarray spot statistics
maColorBar: Calibration bar for color images
maCompCoord: Generate grid and spot matrix coordinates
maCompInd: Generate spot indices
maCompLayout: Generate a marrayLayout object
maCompNormA: Weights for composite normalization
maCompPlate: Generate plate IDs
maCoord2Ind: Convert grid and spot matrix coordinates to spot indices
maDefaultPar: Default graphical parameters for microarray objects
maDotsDefaults: Replace graphical default parameters by user supplied...
maDotsMatch: Replace default arguments of a function by user supplied...
maGenControls: Generating a vector recording the control status of the...
maGeneTable: Table of spot coordinates and gene names
maImage: Color image for cDNA microarray spot statistics
maImage.func: Color image for cDNA microarray spot statistics
maInd2Coord: Convert spot indices to grid and spot matrix coordinates
maLegendLines: Add a legend to a plot
maLoess: Stratified univariate robust local regression
maLoessLines: Add smoothed fits to a plot
maMAD: Stratified MAD calculation
maMed: Stratified median calculation
maNA: Basic Statistical Functions for Handling Missing Values
maNorm: Simple location and scale normalization function
maNorm2D: 2D spatial location normalization function
maNormLoess: Intensity dependent location normalization function
maNormMAD: MAD scale normalization function
maNormMain: Main function for location and scale normalization of cDNA...
maNormMed: Median location normalization function
maNormScale: Simple scale normalization function
maNum2Logic: Convert a numeric vector of indices to a logical vector
maPalette: Microarray color palette
mapGeneInfo: Creating URL strings for external database links
maPlot: Scatter-plots for cDNA microarray spot statistics
maPlot.func: Scatter-plots with fitted curves and text
marrayInfo-class: Class "marrayInfo", description of target samples or spotted...
marray-internal: Internal marray functions
marrayLayout-class: Class "marrayLayout", classes and methods for layout...
marrayNorm-class: Class "marrayNorm", classes and methods for...
marrayRaw-class: Class "marrayRaw", classes and methods for pre-normalization...
maSelectGnames: Select genes according to the values of a few different...
maText: Highlight points on a plot
maTop: Identify extreme values
maTwoSamples: Changing signs for two sample analysis
opVersionID: Determine the operon oligo set ID
plotMA: Scatter-plots for cDNA microarray spot statistics
print-methods: Printing summary methods for microarray objects
read.Galfile: Reading GenePix Gal file
read.marrayInfo: Create objects of class marrayInfo
read.marrayLayout: Create objects of class marrayLayout
read.marrayRaw: Create objects of class "marrayRaw"
rm.na: Remove missing values
showLargeObject: Show Large Data Object - class
stat.confband.text: Rank genes according to the value of a statistic.
stat.gnames: Sort Genes According to the Value of a Statistic
swirl: Gene expression data from Swirl zebrafish cDNA microarray...
write.list: Data Output
write.marray: Data Output
write.xls: Data Output

Functions

SFGL Man page
ShowLargeObject-class Man page
SwirlSample Man page
SwirlSample.txt Man page
UCBFGL Man page
URLstring Man page
[ Man page
[,marrayInfo-method Man page
[,marrayLayout-method Man page
[,marrayNorm-method Man page
[,marrayRaw-method Man page
[-methods Man page
addLines Man page Source code
addPoints Man page Source code
addText Man page Source code
as Man page
boxplot,marrayNorm-method Man page
boxplot,marrayRaw-method Man page
cbind,marrayNorm-method Man page
cbind,marrayRaw-method Man page
cbind.marrayNorm Man page Source code
cbind.marrayRaw Man page Source code
checkTargetInfo Man page Source code
coerce Man page
coerce,marrayNorm,marraySpots-method Man page
coerce,marrayRaw,marrayNorm-method Man page Man page
coerce-methods Man page
controlCode Man page
cor.na Man page Source code
dim.marrayInfo Man page Source code
dim.marrayNorm Man page Source code
dim.marrayRaw Man page Source code
findID Man page Source code
fish.gal Man page
gsubAnchor Man page Source code
htmlPage Man page Source code
image,marrayNorm-method Man page
image,marrayRaw-method Man page
length.na Man page Source code
lines,marrayNorm-method Man page
lines,marrayRaw-method Man page
log.na Man page Source code
ma2D Man page Source code
maA Man page Man page
maA,marrayNorm-method Man page
maA,marrayRaw-method Man page
maA<- Man page
maA<-,marrayNorm,matrix-method Man page
maBoxplot Man page Source code
maColorBar Man page Source code
maCompCoord Man page Source code
maCompInd Man page Source code
maCompLayout Man page Source code
maCompNormA Man page Source code
maCompNormEq Man page Source code
maCompPlate Man page Source code
maControls Man page Man page
maControls,marrayLayout-method Man page
maControls,marrayNorm-method Man page
maControls,marrayRaw-method Man page
maControls<- Man page
maControls<-,marrayLayout-method Man page
maControls<-,marrayNorm-method Man page
maControls<-,marrayRaw-method Man page
maCoord2Ind Man page Source code
maDefaultPar Man page Source code
maDotsDefaults Man page Source code
maDotsMatch Man page Source code
maGb Man page
maGb,marrayRaw-method Man page
maGb<- Man page
maGb<-,marrayRaw,NULL-method Man page
maGb<-,marrayRaw,matrix-method Man page
maGenControls Man page Source code
maGeneTable Man page Source code
maGf Man page
maGf,marrayRaw-method Man page
maGf<- Man page
maGf<-,marrayRaw,matrix-method Man page
maGnames Man page
maGnames,marrayNorm-method Man page
maGnames,marrayRaw-method Man page
maGnames<- Man page
maGnames<-,marrayNorm,marrayInfo-method Man page Man page
maGnames<-,marrayRaw,marrayInfo-method Man page Man page
maGnames<-,marraySpots,marrayInfo-method Man page
maGridCol Man page
maGridCol,marrayLayout-method Man page
maGridCol,marrayNorm-method Man page
maGridCol,marrayRaw-method Man page
maGridRow Man page Man page
maGridRow,marrayLayout-method Man page
maGridRow,marrayNorm-method Man page
maGridRow,marrayRaw-method Man page
maImage Man page Source code
maImage.func Man page Source code
maInd2Coord Man page Source code
maInfo Man page
maInfo,marrayInfo-method Man page
maInfo<- Man page
maInfo<-,marrayInfo,data.frame-method Man page
maLG Man page
maLG,marrayNorm-method Man page
maLG,marrayRaw-method Man page
maLR Man page
maLR,marrayNorm-method Man page
maLR,marrayRaw-method Man page
maLabels Man page
maLabels,marrayInfo-method Man page
maLabels<- Man page
maLabels<-,marrayInfo,character-method Man page
maLabels<-,marrayInfo,numeric-method Man page
maLayout Man page
maLayout,marrayNorm-method Man page
maLayout,marrayRaw-method Man page
maLayout<- Man page
maLayout<-,marrayNorm,marrayLayout-method Man page Man page
maLayout<-,marrayRaw,marrayLayout-method Man page Man page
maLegendLines Man page Source code
maLoess Man page Source code
maLoessLines Man page Source code
maLowessLines Man page Source code
maM Man page Man page
maM,marrayNorm-method Man page
maM,marrayRaw-method Man page
maM<- Man page
maM<-,marrayNorm,matrix-method Man page
maMAD Man page Source code
maMed Man page Source code
maMloc Man page
maMloc,marrayNorm-method Man page
maMloc<- Man page
maMloc<-,marrayNorm,matrix-method Man page
maMscale Man page
maMscale,marrayNorm-method Man page
maMscale<- Man page
maMscale<-,marrayNorm,matrix-method Man page
maNgc Man page Man page
maNgc,marrayLayout-method Man page
maNgc,marrayNorm-method Man page
maNgc,marrayRaw-method Man page
maNgc<- Man page
maNgc<-,marrayLayout,numeric-method Man page
maNgc<-,marrayNorm,numeric-method Man page
maNgc<-,marrayRaw,numeric-method Man page
maNgr Man page Man page
maNgr,marrayLayout-method Man page
maNgr,marrayNorm-method Man page
maNgr,marrayRaw-method Man page
maNgr<- Man page
maNgr<-,marrayLayout,numeric-method Man page
maNgr<-,marrayNorm,numeric-method Man page
maNgr<-,marrayRaw,numeric-method Man page
maNorm Man page Source code
maNorm2D Man page Source code
maNormCall Man page
maNormCall,marrayNorm-method Man page
maNormLoess Man page Source code
maNormMAD Man page Source code
maNormMain Man page Source code
maNormMed Man page Source code
maNormScale Man page Source code
maNotes Man page Man page Man page
maNotes,marrayInfo-method Man page
maNotes,marrayLayout-method Man page
maNotes,marrayNorm-method Man page
maNotes,marrayRaw-method Man page
maNotes<- Man page
maNotes<-,marrayInfo,character-method Man page
maNotes<-,marrayLayout,character-method Man page
maNotes<-,marrayNorm,character-method Man page
maNotes<-,marrayRaw,character-method Man page
maNsamples Man page
maNsamples,marrayNorm-method Man page
maNsamples,marrayRaw-method Man page
maNsc Man page Man page
maNsc,marrayLayout-method Man page
maNsc,marrayNorm-method Man page
maNsc,marrayRaw-method Man page
maNsc<- Man page
maNsc<-,marrayLayout,numeric-method Man page
maNsc<-,marrayNorm,numeric-method Man page
maNsc<-,marrayRaw,numeric-method Man page
maNspots Man page Man page
maNspots,marrayLayout-method Man page
maNspots,marrayNorm-method Man page
maNspots,marrayRaw-method Man page
maNspots<- Man page
maNspots<-,marrayLayout,numeric-method Man page
maNspots<-,marrayNorm,numeric-method Man page
maNspots<-,marrayRaw,numeric-method Man page
maNsr Man page Man page
maNsr,marrayLayout-method Man page
maNsr,marrayNorm-method Man page
maNsr,marrayRaw-method Man page
maNsr<- Man page
maNsr<-,marrayLayout,numeric-method Man page
maNsr<-,marrayNorm,numeric-method Man page
maNsr<-,marrayRaw,numeric-method Man page
maNum2Logic Man page Source code
maPalette Man page Source code
maPlate Man page Man page
maPlate,marrayLayout-method Man page
maPlate,marrayNorm-method Man page
maPlate,marrayRaw-method Man page
maPlate<- Man page
maPlate<-,marrayLayout-method Man page
maPlate<-,marrayNorm-method Man page
maPlate<-,marrayRaw-method Man page
maPlot Man page Source code
maPlot.func Man page Source code
maPrintTip Man page Man page
maPrintTip,marrayLayout-method Man page
maPrintTip,marrayNorm-method Man page
maPrintTip,marrayRaw-method Man page
maRb Man page
maRb,marrayRaw-method Man page
maRb<- Man page
maRb<-,marrayRaw,NULL-method Man page
maRb<-,marrayRaw,matrix-method Man page
maRf Man page
maRf,marrayRaw-method Man page
maRf<- Man page
maRf<-,marrayRaw,matrix-method Man page
maSelectGnames Man page Source code
maSpotCol Man page Man page
maSpotCol,marrayLayout-method Man page
maSpotCol,marrayNorm-method Man page
maSpotCol,marrayRaw-method Man page
maSpotRow Man page Man page
maSpotRow,marrayLayout-method Man page
maSpotRow,marrayNorm-method Man page
maSpotRow,marrayRaw-method Man page
maSub Man page Man page
maSub,marrayLayout-method Man page
maSub,marrayNorm-method Man page
maSub,marrayRaw-method Man page
maSub<- Man page
maSub<-,marrayLayout,logical-method Man page
maSub<-,marrayLayout,numeric-method Man page
maSub<-,marrayNorm-method Man page
maSub<-,marrayRaw-method Man page
maTargets Man page
maTargets,marrayNorm-method Man page
maTargets,marrayRaw-method Man page
maTargets<- Man page
maTargets<-,marrayNorm,marrayInfo-method Man page Man page
maTargets<-,marrayRaw,marrayInfo-method Man page Man page
maText Man page Source code
maTop Man page Source code
maTwoSamples Man page Source code
maW Man page
maW,marrayNorm-method Man page
maW,marrayRaw-method Man page
maW<- Man page
maW<-,marrayNorm,matrix-method Man page
maW<-,marrayRaw,matrix-method Man page
mapGeneInfo Man page Source code
marrayInfo Man page
marrayInfo-class Man page
marrayLayout Man page
marrayLayout-class Man page
marrayNorm Man page
marrayNorm-class Man page
marrayRaw Man page
marrayRaw-class Man page
mean.na Man page Source code
opVersionID Man page Source code
order.na Man page Source code
plot.gene.cluster Man page
plot.marrayNorm Man page Source code
plot.marrayRaw Man page Source code
points,marrayNorm-method Man page
points,marrayRaw-method Man page
print Man page
print,marrayInfo-method Man page
print,marrayLayout-method Man page
print,marrayNorm-method Man page
print,marrayRaw-method Man page
print-methods Man page Man page
prod.na Man page Source code
quantile.na Man page Source code
rbind,marrayInfo-method Man page
rbind.marrayInfo Man page Source code
read.Agilent Man page Source code
read.Galfile Man page Source code
read.GenePix Man page Source code
read.SMD Man page Source code
read.Spot Man page Source code
read.fname Man page Source code
read.marrayInfo Man page Source code
read.marrayLayout Man page Source code
read.marrayRaw Man page Source code
rm.na Man page Source code
scale.na Man page Source code
show,ShowLargeObject-method Man page
show,marrayNorm-method Man page
show,marrayRaw-method Man page
show-methods Man page
stat.confband.text Man page Source code
stat.gene.cluster Man page
stat.gnames Man page Source code
sum.na Man page Source code
summary,marrayInfo-method Man page
summary,marrayLayout-method Man page
summary,marrayNorm-method Man page
summary,marrayRaw-method Man page
summary-methods Man page
swirl Man page
swirl.1.spot Man page
swirl.2.spot Man page
swirl.3.spot Man page
swirl.4.spot Man page
table2html Man page Source code
tablegen Man page Source code
text,marrayNorm-method Man page
text,marrayRaw-method Man page
var.na Man page Source code
widget.TwoSamples Man page Source code
widget.mapGeneInfo Man page Source code
widget.marrayInfo Man page Source code
widget.marrayLayout Man page Source code
widget.marrayRaw Man page Source code
write.list Man page Source code
write.marray Man page Source code
write.xls Man page Source code

Files

DESCRIPTION
LICENSE
NAMESPACE
R
R/maAnnotate.R
R/maBind.R
R/maClasses.R
R/maComp.R
R/maDots.R
R/maGet.R
R/maInput.R
R/maNorm.R
R/maOutput.R
R/maPlots.R
R/maPrint.R
R/maRankGenes.R
R/maSMA.R
R/maSearch.R
R/maSet.R
R/maSubset.R
R/maWidget.R
R/maWrap.R
build
build/vignette.rds
data
data/swirl.RData
inst
inst/doc
inst/doc/marray.R
inst/doc/marray.Rnw
inst/doc/marray.pdf
inst/doc/marrayClasses.R
inst/doc/marrayClasses.Rnw
inst/doc/marrayClasses.pdf
inst/doc/marrayClassesShort.R
inst/doc/marrayClassesShort.Rnw
inst/doc/marrayClassesShort.pdf
inst/doc/marrayInput.R
inst/doc/marrayInput.Rnw
inst/doc/marrayInput.pdf
inst/doc/marrayNorm.R
inst/doc/marrayNorm.Rnw
inst/doc/marrayNorm.pdf
inst/doc/marrayPlots.R
inst/doc/marrayPlots.Rnw
inst/doc/marrayPlots.pdf
inst/swirldata
inst/swirldata/SwirlSample.txt
inst/swirldata/fish.gal
inst/swirldata/swirl.1.spot
inst/swirldata/swirl.2.spot
inst/swirldata/swirl.3.spot
inst/swirldata/swirl.4.spot
man
man/boxplot.Rd
man/bracketMethods.Rd
man/cbind.Rd
man/checkTargetInfo.Rd
man/coerce-methods.Rd
man/dim.Rd
man/findID.Rd
man/htmlPage.Rd
man/image.Rd
man/ma2D.Rd
man/maBoxplot.Rd
man/maColorBar.Rd
man/maCompCoord.Rd
man/maCompInd.Rd
man/maCompLayout.Rd
man/maCompNormA.Rd
man/maCompPlate.Rd
man/maCoord2Ind.Rd
man/maDefaultPar.Rd
man/maDotsDefaults.Rd
man/maDotsMatch.Rd
man/maGenControls.Rd
man/maGeneTable.Rd
man/maImage.Rd
man/maImage.func.Rd
man/maInd2Coord.Rd
man/maLegendLines.Rd
man/maLoess.Rd
man/maLoessLines.Rd
man/maMAD.Rd
man/maMed.Rd
man/maNA.Rd
man/maNorm.Rd
man/maNorm2D.Rd
man/maNormLoess.Rd
man/maNormMAD.Rd
man/maNormMain.Rd
man/maNormMed.Rd
man/maNormScale.Rd
man/maNum2Logic.Rd
man/maPalette.Rd
man/maPlot.Rd
man/maPlot.func.Rd
man/maSelectGnames.Rd
man/maText.Rd
man/maTop.Rd
man/maTwoSamples.Rd
man/mapGeneInfo.Rd
man/marray-internal.Rd
man/marrayInfo-class.Rd
man/marrayLayout-class.Rd
man/marrayNorm-class.Rd
man/marrayRaw-class.Rd
man/opVersionID.Rd
man/plotMA.Rd
man/print-methods.Rd
man/read.Galfile.Rd
man/read.marrayInfo.Rd
man/read.marrayLayout.Rd
man/read.marrayRaw.Rd
man/rm.na.Rd
man/showLargeObject.Rd
man/stat.confband.text.Rd
man/stat.gnames.Rd
man/swirl.Rd
man/write.list.Rd
man/write.marray.Rd
man/write.xls.Rd
marray.hist
vignettes
vignettes/ExampleHTML.pdf
vignettes/marray.Rnw
vignettes/marrayClasses.Rnw
vignettes/marrayClassesShort.Rnw
vignettes/marrayInput.Rnw
vignettes/marrayNorm.Rnw
vignettes/marrayPacks.bib
vignettes/marrayPlots.Rnw
vignettes/widget1.pdf
vignettes/widget1.ps
vignettes/widgetmaStat.png
vignettes/widgetmapGeneInfo.png
marray documentation built on May 20, 2017, 10:12 p.m.

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