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.

Author
Yee Hwa (Jean) Yang <jeany@maths.usyd.edu.au> with contributions from Agnes Paquet and Sandrine Dudoit.
Date of publication
None
Maintainer
Yee Hwa (Jean) Yang <jean@biostat.ucsf.edu>
License
LGPL
Version
1.52.0
URLs

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

Files in this package

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