marray: Exploratory analysis for two-color spotted microarray data

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.
Date of publicationNone
MaintainerYee Hwa (Jean) Yang <jean@biostat.ucsf.edu>
LicenseLGPL
Version1.52.0
http://www.maths.usyd.edu.au/u/jeany/

View on Bioconductor

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

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

Files

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

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