Function	Description
boxplot,marrayRaw-method	Boxplots for cDNA microarray spot statistics
cbind.marrayRaw	Combine marrayRaw, marrayNorm or marrayInfo Objects
checkTargetInfo	Verifying the order between intensities matrix and target file information
coerce-methods	Coerce an object to belong to a given microarray class
dim.marrayRaw	Retrieve the Dimensions of an marrayRaw, marrayNorm or marrayInfo Object
findID	Find ID when given an accession number
htmlPage	Display gene list as a HTML page
image,marrayRaw-method	Color image for cDNA microarray spot statistics
log.na	Basic Statistical Functions for Handling Missing Values
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 parameters
maDotsMatch	Replace default arguments of a function by user supplied values
maGenControls	Generating a vector recording the control status of the spotted probe sequences.
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
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 microarray data
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 probe sequences
marrayLayout-class	Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays
marrayNorm-class	Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data
marrayRaw-class	Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
maSelectGnames	Select genes according to the values of a few different statistics
maText	Highlight points on a plot
maTop	Identify extreme values
maTwoSamples	Changing signs for two sample analysis
[-methods	Subsetting methods for microarray objects
opVersionID	Determine the operon oligo set ID
plot.marrayRaw	Scatter-plots for cDNA microarray spot statistics
read.fname	Internal marray functions
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-class	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
summary-methods	Printing summary methods for microarray objects
swirl	Gene expression data from Swirl zebrafish cDNA microarray experiment
write.list	Data Output
write.marray	Data Output
write.xls	Data Output