ShowLargeObject-class   Show Large Data Object - class
[-methods               Subsetting methods for microarray objects
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
maPlot                  Scatter-plots for cDNA microarray spot
                        statistics
maPlot.func             Scatter-plots with fitted curves and text
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
mapGeneInfo             Creating URL strings for external database
                        links
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
opVersionID             Determine the operon oligo set ID
plot.marrayRaw          Scatter-plots for cDNA microarray spot
                        statistics
read.Galfile            Reading GenePix Gal file
read.fname              Internal marray functions
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
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