Entry: boxplot
Aliases: boxplot,marrayRaw-method boxplot,marrayNorm-method
Keywords: hplot
Description: Boxplots for cDNA microarray spot statistics
URL: ../../../library/marray/html/boxplot.html

Entry: [-methods
Aliases: [-methods [
Keywords: methods
Description: Subsetting methods for microarray objects
URL: ../../../library/marray/html/bracketMethods.html

Entry: cbind
Aliases: cbind.marrayRaw cbind.marrayNorm rbind.marrayInfo
Keywords: manip
Description: Combine marrayRaw, marrayNorm or marrayInfo Objects
URL: ../../../library/marray/html/cbind.html

Entry: checkTargetInfo
Aliases: checkTargetInfo
Keywords: file
Description: Verifying the order between intensities matrix and target file information
URL: ../../../library/marray/html/checkTargetInfo.html

Entry: coerce-methods
Aliases: coerce-methods coerce as
Keywords: methods
Description: Coerce an object to belong to a given microarray class
URL: ../../../library/marray/html/coerce-methods.html

Entry: dim
Aliases: dim.marrayRaw dim.marrayNorm dim.marrayInfo
Keywords: array
Description: Retrieve the Dimensions of an marrayRaw, marrayNorm or marrayInfo Object
URL: ../../../library/marray/html/dim.html

Entry: findID
Aliases: findID
Keywords: manip
Description: Find ID when given an accession number
URL: ../../../library/marray/html/findID.html

Entry: htmlPage
Aliases: htmlPage table2html
Keywords: file
Description: Display gene list as a HTML page
URL: ../../../library/marray/html/htmlPage.html

Entry: image
Aliases: image,marrayRaw-method image,marrayNorm-method
Keywords: hplot
Description: Color image for cDNA microarray spot statistics
URL: ../../../library/marray/html/image.html

Entry: ma2D
Aliases: ma2D
Keywords: smooth
Description: Stratified bivariate robust local regression
URL: ../../../library/marray/html/ma2D.html

Entry: maBoxplot
Aliases: maBoxplot
Keywords: hplot
Description: Boxplots for cDNA microarray spot statistics
URL: ../../../library/marray/html/maBoxplot.html

Entry: maColorBar
Aliases: maColorBar
Keywords: aplot hplot
Description: Calibration bar for color images
URL: ../../../library/marray/html/maColorBar.html

Entry: maCompCoord
Aliases: maCompCoord
Keywords: manip methods
Description: Generate grid and spot matrix coordinates
URL: ../../../library/marray/html/maCompCoord.html

Entry: maCompInd
Aliases: maCompInd
Keywords: manip methods
Description: Generate spot indices
URL: ../../../library/marray/html/maCompInd.html

Entry: maCompLayout
Aliases: maCompLayout
Keywords: manip
Description: Generate a marrayLayout object
URL: ../../../library/marray/html/maCompLayout.html

Entry: maCompNormA
Aliases: maCompNormA maCompNormEq
Keywords: smooth
Description: Weights for composite normalization
URL: ../../../library/marray/html/maCompNormA.html

Entry: maCompPlate
Aliases: maCompPlate
Keywords: methods
Description: Generate plate IDs
URL: ../../../library/marray/html/maCompPlate.html

Entry: maCoord2Ind
Aliases: maCoord2Ind
Keywords: manip methods
Description: Convert grid and spot matrix coordinates to spot indices
URL: ../../../library/marray/html/maCoord2Ind.html

Entry: maDefaultPar
Aliases: maDefaultPar
Keywords: iplot dplot color
Description: Default graphical parameters for microarray objects
URL: ../../../library/marray/html/maDefaultPar.html

Entry: maDotsDefaults
Aliases: maDotsDefaults
Keywords: misc
Description: Replace graphical default parameters by user supplied parameters
URL: ../../../library/marray/html/maDotsDefaults.html

Entry: maDotsMatch
Aliases: maDotsMatch
Keywords: misc
Description: Replace default arguments of a function by user supplied values
URL: ../../../library/marray/html/maDotsMatch.html

Entry: maGenControls
Aliases: maGenControls controlCode
Keywords: manip
Description: Generating a vector recording the control status of the spotted probe sequences.
URL: ../../../library/marray/html/maGenControls.html

Entry: maGeneTable
Aliases: maGeneTable
Keywords: methods
Description: Table of spot coordinates and gene names
URL: ../../../library/marray/html/maGeneTable.html

Entry: maImage
Aliases: maImage
Keywords: hplot
Description: Color image for cDNA microarray spot statistics
URL: ../../../library/marray/html/maImage.html

Entry: maImage.func
Aliases: maImage.func
Keywords: hplot
Description: Color image for cDNA microarray spot statistics
URL: ../../../library/marray/html/maImage.func.html

Entry: maInd2Coord
Aliases: maInd2Coord
Keywords: manip methods
Description: Convert spot indices to grid and spot matrix coordinates
URL: ../../../library/marray/html/maInd2Coord.html

Entry: maLegendLines
Aliases: maLegendLines
Keywords: aplot
Description: Add a legend to a plot
URL: ../../../library/marray/html/maLegendLines.html

Entry: maLoess
Aliases: maLoess
Keywords: smooth
Description: Stratified univariate robust local regression
URL: ../../../library/marray/html/maLoess.html

Entry: maLoessLines
Aliases: maLoessLines maLowessLines
Keywords: aplot smooth
Description: Add smoothed fits to a plot
URL: ../../../library/marray/html/maLoessLines.html

Entry: maMAD
Aliases: maMAD
Keywords: univar robust
Description: Stratified MAD calculation
URL: ../../../library/marray/html/maMAD.html

Entry: maMed
Aliases: maMed
Keywords: univar robust
Description: Stratified median calculation
URL: ../../../library/marray/html/maMed.html

Entry: na
Aliases: log.na sum.na mean.na var.na cor.na quantile.na length.na order.na scale.na prod.na
Keywords: arith
Description: Basic Statistical Functions for Handling Missing Values
URL: ../../../library/marray/html/maNA.html

Entry: maNorm
Aliases: maNorm
Keywords: smooth methods
Description: Simple location and scale normalization function
URL: ../../../library/marray/html/maNorm.html

Entry: maNorm2D
Aliases: maNorm2D
Keywords: smooth
Description: 2D spatial location normalization function
URL: ../../../library/marray/html/maNorm2D.html

Entry: maNormLoess
Aliases: maNormLoess
Keywords: smooth
Description: Intensity dependent location normalization function
URL: ../../../library/marray/html/maNormLoess.html

Entry: maNormMAD
Aliases: maNormMAD
Keywords: univar robust
Description: MAD scale normalization function
URL: ../../../library/marray/html/maNormMAD.html

Entry: maNormMain
Aliases: maNormMain
Keywords: smooth methods
Description: Main function for location and scale normalization of cDNA microarray data
URL: ../../../library/marray/html/maNormMain.html

Entry: maNormMed
Aliases: maNormMed
Keywords: univar robust
Description: Median location normalization function
URL: ../../../library/marray/html/maNormMed.html

Entry: maNormScale
Aliases: maNormScale
Keywords: smooth methods
Description: Simple scale normalization function
URL: ../../../library/marray/html/maNormScale.html

Entry: maNum2Logic
Aliases: maNum2Logic
Keywords: manip
Description: Convert a numeric vector of indices to a logical vector
URL: ../../../library/marray/html/maNum2Logic.html

Entry: maPalette
Aliases: maPalette
Keywords: color
Description: Microarray color palette
URL: ../../../library/marray/html/maPalette.html

Entry: maPlot
Aliases: maPlot
Keywords: hplot
Description: Scatter-plots for cDNA microarray spot statistics
URL: ../../../library/marray/html/maPlot.html

Entry: maPlot.func
Aliases: maPlot.func
Keywords: hplot
Description: Scatter-plots with fitted curves and text
URL: ../../../library/marray/html/maPlot.func.html

Entry: maSelectGnames
Aliases: maSelectGnames
Keywords: manip
Description: Select genes according to the values of a few different statistics
URL: ../../../library/marray/html/maSelectGnames.html

Entry: maText
Aliases: maText
Keywords: aplot
Description: Highlight points on a plot
URL: ../../../library/marray/html/maText.html

Entry: maTop
Aliases: maTop
Keywords: misc
Description: Identify extreme values
URL: ../../../library/marray/html/maTop.html

Entry: maTwoSamples
Aliases: maTwoSamples widget.TwoSamples
Keywords: manip
Description: Changing signs for two sample analysis
URL: ../../../library/marray/html/maTwoSamples.html

Entry: mapGeneInfo
Aliases: mapGeneInfo widget.mapGeneInfo URLstring SFGL UCBFGL
Keywords: manip
Description: Creating URL strings for external database links
URL: ../../../library/marray/html/mapGeneInfo.html

Entry: Internal functions
Aliases: read.fname stat.gene.cluster plot.gene.cluster tablegen gsubAnchor
Keywords: methods
Description: Internal marray functions
URL: ../../../library/marray/html/marray-internal.html

Entry: marrayInfo-class
Aliases: marrayInfo-class marrayInfo maLabels maLabels<- maInfo maInfo<- maNotes maNotes<- [,marrayInfo-method maGnames<-,marrayRaw,marrayInfo-method maGnames<-,marrayNorm,marrayInfo-method maGnames<-,marraySpots,marrayInfo-method maInfo<-,marrayInfo,data.frame-method maInfo,marrayInfo-method maLabels<-,marrayInfo,character-method maLabels<-,marrayInfo,numeric-method maLabels,marrayInfo-method maNotes<-,marrayInfo,character-method maNotes,marrayInfo-method maTargets<-,marrayRaw,marrayInfo-method maTargets<-,marrayNorm,marrayInfo-method print,marrayInfo-method rbind,marrayInfo-method summary,marrayInfo-method
Keywords: classes
Description: Class "marrayInfo", description of target samples or spotted probe sequences
URL: ../../../library/marray/html/marrayInfo-class.html

Entry: marrayLayout-class
Aliases: marrayLayout-class marrayLayout maNgr maNgr<- maNgc maNgc<- maNsr maNsr<- maNsc maNsc<- maNspots maNspots<- maSub maSub<- maPlate maPlate<- maControls maControls<- [,marrayLayout-method maControls<-,marrayLayout-method maControls,marrayLayout-method maGridCol,marrayLayout-method maGridRow,marrayLayout-method maLayout<-,marrayRaw,marrayLayout-method maLayout<-,marrayNorm,marrayLayout-method maNgc<-,marrayLayout,numeric-method maNgc,marrayLayout-method maNgr<-,marrayLayout,numeric-method maNgr,marrayLayout-method maNotes<-,marrayLayout,character-method maNotes,marrayLayout-method maNsc<-,marrayLayout,numeric-method maNsc,marrayLayout-method maNspots<-,marrayLayout,numeric-method maNspots,marrayLayout-method maNsr<-,marrayLayout,numeric-method maNsr,marrayLayout-method maPlate<-,marrayLayout-method maPlate,marrayLayout-method maPrintTip,marrayLayout-method maSpotCol,marrayLayout-method maSpotRow,marrayLayout-method maSub<-,marrayLayout,logical-method maSub<-,marrayLayout,numeric-method maSub,marrayLayout-method print,marrayLayout-method summary,marrayLayout-method maPrintTip maGridRow maGridCol maSpotRow maSpotCol
Keywords: classes
Description: Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays
URL: ../../../library/marray/html/marrayLayout-class.html

Entry: marrayNorm-class
Aliases: marrayNorm-class marrayNorm maA maA<- maM maM<- maMloc maMloc<- maMscale maMscale<- [,marrayNorm-method cbind,marrayNorm-method coerce,marrayRaw,marrayNorm-method maA<-,marrayNorm,matrix-method maA,marrayNorm-method maControls<-,marrayNorm-method maControls,marrayNorm-method maGnames,marrayNorm-method maGridCol,marrayNorm-method maGridRow,marrayNorm-method maLayout,marrayNorm-method maMloc<-,marrayNorm,matrix-method maMloc,marrayNorm-method maM<-,marrayNorm,matrix-method maM,marrayNorm-method maMscale<-,marrayNorm,matrix-method maMscale,marrayNorm-method maNgc<-,marrayNorm,numeric-method maNgc,marrayNorm-method maNgr<-,marrayNorm,numeric-method maNgr,marrayNorm-method maNormCall,marrayNorm-method maNotes<-,marrayNorm,character-method maNotes,marrayNorm-method maNsamples,marrayNorm-method maNsc<-,marrayNorm,numeric-method maNsc,marrayNorm-method maNspots<-,marrayNorm,numeric-method maNspots,marrayNorm-method maNsr<-,marrayNorm,numeric-method maNsr,marrayNorm-method maPlate<-,marrayNorm-method maPlate,marrayNorm-method maPrintTip,marrayNorm-method maSpotCol,marrayNorm-method maSpotRow,marrayNorm-method maSub<-,marrayNorm-method maSub,marrayNorm-method maTargets,marrayNorm-method maW<-,marrayNorm,matrix-method maW,marrayNorm-method maLG,marrayNorm-method maLR,marrayNorm-method print,marrayNorm-method show,marrayNorm-method summary,marrayNorm-method maNormCall
Keywords: classes
Description: Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data
URL: ../../../library/marray/html/marrayNorm-class.html

Entry: marrayRaw-class
Aliases: marrayRaw-class marrayRaw maRf maRf<- maGf maGf<- maRb maRb<- maGb maGb<- maW maW<- maLayout maLayout<- [,marrayRaw-method cbind,marrayRaw-method maA,marrayRaw-method maControls<-,marrayRaw-method maControls,marrayRaw-method maGb<-,marrayRaw,matrix-method maGb<-,marrayRaw,NULL-method maGb,marrayRaw-method maGf<-,marrayRaw,matrix-method maGf,marrayRaw-method maGnames,marrayRaw-method maGridCol,marrayRaw-method maGridRow,marrayRaw-method maLayout,marrayRaw-method maLG,marrayRaw-method maLR,marrayRaw-method maM,marrayRaw-method maNgc<-,marrayRaw,numeric-method maNgc,marrayRaw-method maNgr<-,marrayRaw,numeric-method maNgr,marrayRaw-method maNotes<-,marrayRaw,character-method maNotes,marrayRaw-method maNsamples,marrayRaw-method maNsc<-,marrayRaw,numeric-method maNsc,marrayRaw-method maNspots<-,marrayRaw,numeric-method maNspots,marrayRaw-method maNsr<-,marrayRaw,numeric-method maNsr,marrayRaw-method maPlate<-,marrayRaw-method maPlate,marrayRaw-method maPrintTip,marrayRaw-method maRb<-,marrayRaw,matrix-method maRb<-,marrayRaw,NULL-method maRb,marrayRaw-method maRf<-,marrayRaw,matrix-method maRf,marrayRaw-method maSpotCol,marrayRaw-method maSpotRow,marrayRaw-method maSub<-,marrayRaw-method maSub,marrayRaw-method maTargets,marrayRaw-method maW<-,marrayRaw,matrix-method maW,marrayRaw-method print,marrayRaw-method show,marrayRaw-method summary,marrayRaw-method maGnames maGnames<- maTargets maTargets<- maLR maLG maNsamples
Keywords: classes
Description: Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
URL: ../../../library/marray/html/marrayRaw-class.html

Entry: opVersionID
Aliases: opVersionID
Keywords: manip
Description: Determine the operon oligo set ID
URL: ../../../library/marray/html/opVersionID.html

Entry: plot
Aliases: plot.marrayRaw plot.marrayNorm addText addLines addPoints text,marrayRaw-method text,marrayNorm-method lines,marrayRaw-method lines,marrayNorm-method points,marrayRaw-method points,marrayNorm-method
Keywords: hplot
Description: Scatter-plots for cDNA microarray spot statistics
URL: ../../../library/marray/html/plotMA.html

Entry: summary-methods
Aliases: summary-methods
Keywords: methods
Description: Printing summary methods for microarray objects
URL: ../../../library/marray/html/print-methods.html

Entry: read.Galfile
Aliases: read.Galfile
Keywords: file
Description: Reading GenePix Gal file
URL: ../../../library/marray/html/read.Galfile.html

Entry: read.marrayInfo
Aliases: read.marrayInfo widget.marrayInfo
Keywords: file connection
Description: Create objects of class marrayInfo
URL: ../../../library/marray/html/read.marrayInfo.html

Entry: read.marrayLayout
Aliases: read.marrayLayout widget.marrayLayout
Keywords: file connection
Description: Create objects of class marrayLayout
URL: ../../../library/marray/html/read.marrayLayout.html

Entry: read.marrayRaw
Aliases: read.marrayRaw read.Spot read.GenePix read.SMD read.Agilent widget.marrayRaw
Keywords: file
Description: Create objects of class "marrayRaw"
URL: ../../../library/marray/html/read.marrayRaw.html

Entry: rm.na
Aliases: rm.na
Keywords: manip
Description: Remove missing values
URL: ../../../library/marray/html/rm.na.html

Entry: ShowLargeObject-class
Aliases: ShowLargeObject-class show,ShowLargeObject-method
Keywords: classes data
Description: Show Large Data Object - class
URL: ../../../library/marray/html/showLargeObject.html

Entry: stat.confband.text
Aliases: stat.confband.text
Keywords: manip
Description: Rank genes according to the value of a statistic.
URL: ../../../library/marray/html/stat.confband.text.html

Entry: stat.gnames
Aliases: stat.gnames
Keywords: misc
Description: Sort Genes According to the Value of a Statistic
URL: ../../../library/marray/html/stat.gnames.html

Entry: swirl
Aliases: swirl swirl.1.spot swirl.2.spot swirl.3.spot swirl.4.spot fish.gal SwirlSample.txt SwirlSample
Keywords: datasets
Description: Gene expression data from Swirl zebrafish cDNA microarray experiment
URL: ../../../library/marray/html/swirl.html

Entry: write.list
Aliases: write.list
Keywords: file
Description: Data Output
URL: ../../../library/marray/html/write.list.html

Entry: write.marray
Aliases: write.marray
Keywords: file
Description: Data Output
URL: ../../../library/marray/html/write.marray.html

Entry: write.xls
Aliases: write.xls
Keywords: file
Description: Data Output
URL: ../../../library/marray/html/write.xls.html