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

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

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