# Exploratory analysis for two-color spotted microarray data

## Documentation for package ‘marray’ version 1.24.0

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

A B C D F G H I L M O P Q R S T U V W misc

## -- A --

addLines | Scatter-plots for cDNA microarray spot statistics
addPoints | Scatter-plots for cDNA microarray spot statistics
addText | Scatter-plots for cDNA microarray spot statistics
as | Coerce an object to belong to a given microarray class

## -- B --

boxplot,marrayNorm-method | Boxplots for cDNA microarray spot statistics
boxplot,marrayRaw-method | Boxplots for cDNA microarray spot statistics

## -- C --

cbind,marrayNorm-method | Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data
cbind,marrayRaw-method | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
cbind.marrayNorm | Combine marrayRaw, marrayNorm or marrayInfo Objects
cbind.marrayRaw | Combine marrayRaw, marrayNorm or marrayInfo Objects
checkTargetInfo | Verifying the order between intensities matrix and target file information
coerce | Coerce an object to belong to a given microarray class
coerce,marrayRaw,marrayNorm-method | Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data
coerce-methods | Coerce an object to belong to a given microarray class
controlCode | Generating a vector recording the control status of the spotted probe sequences.
cor.na | Basic Statistical Functions for Handling Missing Values

## -- D --

dim.marrayInfo | Retrieve the Dimensions of an marrayRaw, marrayNorm or marrayInfo Object
dim.marrayNorm | Retrieve the Dimensions of an marrayRaw, marrayNorm or marrayInfo Object
dim.marrayRaw | Retrieve the Dimensions of an marrayRaw, marrayNorm or marrayInfo Object

## -- F --

findID | Find ID when given an accession number
fish.gal | Gene expression data from Swirl zebrafish cDNA microarray experiment

## -- G --

gsubAnchor | Internal marray functions

## -- H --

htmlPage | Display gene list as a HTML page

## -- I --

image,marrayNorm-method | Color image for cDNA microarray spot statistics
image,marrayRaw-method | Color image for cDNA microarray spot statistics

## -- L --

length.na | Basic Statistical Functions for Handling Missing Values
lines,marrayNorm-method | Scatter-plots for cDNA microarray spot statistics
lines,marrayRaw-method | Scatter-plots for cDNA microarray spot statistics
log.na | Basic Statistical Functions for Handling Missing Values

## -- M --

ma2D | Stratified bivariate robust local regression
maA | Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data
maA,marrayNorm-method | Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data
maA,marrayRaw-method | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
maA<- | Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data
maA<-,marrayNorm,matrix-method | Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data
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
maCompNormEq | Weights for composite normalization
maCompPlate | Generate plate IDs
maControls | Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays
maControls,marrayLayout-method | Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays
maControls,marrayNorm-method | Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data
maControls,marrayRaw-method | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
maControls<- | Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays
maControls<-,marrayLayout-method | Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays
maControls<-,marrayNorm-method | Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data
maControls<-,marrayRaw-method | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
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
maGb | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
maGb,marrayRaw-method | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
maGb<- | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
maGb<-,marrayRaw,matrix-method | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
maGb<-,marrayRaw,NULL-method | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
maGenControls | Generating a vector recording the control status of the spotted probe sequences.
maGeneTable | Table of spot coordinates and gene names
maGf | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
maGf,marrayRaw-method | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
maGf<- | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
maGf<-,marrayRaw,matrix-method | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
maGnames | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
maGnames,marrayNorm-method | Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data
maGnames,marrayRaw-method | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
maGnames<- | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
maGnames<-,marrayNorm,marrayInfo-method | Class "marrayInfo", description of target samples or spotted probe sequences
maGnames<-,marrayRaw,marrayInfo-method | Class "marrayInfo", description of target samples or spotted probe sequences
maGnames<-,marraySpots,marrayInfo-method | Class "marrayInfo", description of target samples or spotted probe sequences
maGridCol | Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays
maGridCol,marrayLayout-method | Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays
maGridCol,marrayNorm-method | Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data
maGridCol,marrayRaw-method | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
maGridRow | Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays
maGridRow,marrayLayout-method | Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays
maGridRow,marrayNorm-method | Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data
maGridRow,marrayRaw-method | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
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
maInfo | Class "marrayInfo", description of target samples or spotted probe sequences
maInfo,marrayInfo-method | Class "marrayInfo", description of target samples or spotted probe sequences
maInfo<- | Class "marrayInfo", description of target samples or spotted probe sequences
maInfo<-,marrayInfo,data.frame-method | Class "marrayInfo", description of target samples or spotted probe sequences
maLabels | Class "marrayInfo", description of target samples or spotted probe sequences
maLabels,marrayInfo-method | Class "marrayInfo", description of target samples or spotted probe sequences
maLabels<- | Class "marrayInfo", description of target samples or spotted probe sequences
maLabels<-,marrayInfo,character-method | Class "marrayInfo", description of target samples or spotted probe sequences
maLabels<-,marrayInfo,numeric-method | Class "marrayInfo", description of target samples or spotted probe sequences
maLayout | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
maLayout,marrayNorm-method | Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data
maLayout,marrayRaw-method | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
maLayout<- | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
maLayout<-,marrayNorm,marrayLayout-method | Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays
maLayout<-,marrayRaw,marrayLayout-method | Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays
maLegendLines | Add a legend to a plot
maLG | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
maLG,marrayNorm-method | Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data
maLG,marrayRaw-method | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
maLoess | Stratified univariate robust local regression
maLoessLines | Add smoothed fits to a plot
maLowessLines | Add smoothed fits to a plot
maLR | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
maLR,marrayNorm-method | Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data
maLR,marrayRaw-method | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
maM | Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data
maM,marrayNorm-method | Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data
maM,marrayRaw-method | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
maM<- | Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data
maM<-,marrayNorm,matrix-method | Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data
maMAD | Stratified MAD calculation
maMed | Stratified median calculation
maMloc | Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data
maMloc,marrayNorm-method | Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data
maMloc<- | Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data
maMloc<-,marrayNorm,matrix-method | Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data
maMscale | Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data
maMscale,marrayNorm-method | Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data
maMscale<- | Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data
maMscale<-,marrayNorm,matrix-method | Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data
maNgc | Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays
maNgc,marrayLayout-method | Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays
maNgc,marrayNorm-method | Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data
maNgc,marrayRaw-method | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
maNgc<- | Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays
maNgc<-,marrayLayout,numeric-method | Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays
maNgc<-,marrayNorm,numeric-method | Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data
maNgc<-,marrayRaw,numeric-method | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
maNgr | Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays
maNgr,marrayLayout-method | Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays
maNgr,marrayNorm-method | Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data
maNgr,marrayRaw-method | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
maNgr<- | Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays
maNgr<-,marrayLayout,numeric-method | Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays
maNgr<-,marrayNorm,numeric-method | Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data
maNgr<-,marrayRaw,numeric-method | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
maNorm | Simple location and scale normalization function
maNorm2D | 2D spatial location normalization function
maNormCall | Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data
maNormCall,marrayNorm-method | Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data
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
maNotes | Class "marrayInfo", description of target samples or spotted probe sequences
maNotes,marrayInfo-method | Class "marrayInfo", description of target samples or spotted probe sequences
maNotes,marrayLayout-method | Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays
maNotes,marrayNorm-method | Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data
maNotes,marrayRaw-method | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
maNotes<- | Class "marrayInfo", description of target samples or spotted probe sequences
maNotes<-,marrayInfo,character-method | Class "marrayInfo", description of target samples or spotted probe sequences
maNotes<-,marrayLayout,character-method | Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays
maNotes<-,marrayNorm,character-method | Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data
maNotes<-,marrayRaw,character-method | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
maNsamples | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
maNsamples,marrayNorm-method | Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data
maNsamples,marrayRaw-method | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
maNsc | Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays
maNsc,marrayLayout-method | Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays
maNsc,marrayNorm-method | Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data
maNsc,marrayRaw-method | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
maNsc<- | Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays
maNsc<-,marrayLayout,numeric-method | Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays
maNsc<-,marrayNorm,numeric-method | Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data
maNsc<-,marrayRaw,numeric-method | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
maNspots | Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays
maNspots,marrayLayout-method | Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays
maNspots,marrayNorm-method | Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data
maNspots,marrayRaw-method | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
maNspots<- | Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays
maNspots<-,marrayLayout,numeric-method | Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays
maNspots<-,marrayNorm,numeric-method | Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data
maNspots<-,marrayRaw,numeric-method | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
maNsr | Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays
maNsr,marrayLayout-method | Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays
maNsr,marrayNorm-method | Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data
maNsr,marrayRaw-method | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
maNsr<- | Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays
maNsr<-,marrayLayout,numeric-method | Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays
maNsr<-,marrayNorm,numeric-method | Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data
maNsr<-,marrayRaw,numeric-method | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
maNum2Logic | Convert a numeric vector of indices to a logical vector
maPalette | Microarray color palette
mapGeneInfo | Creating URL strings for external database links
maPlate | Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays
maPlate,marrayLayout-method | Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays
maPlate,marrayNorm-method | Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data
maPlate,marrayRaw-method | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
maPlate<- | Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays
maPlate<-,marrayLayout-method | Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays
maPlate<-,marrayNorm-method | Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data
maPlate<-,marrayRaw-method | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
maPlot | Scatter-plots for cDNA microarray spot statistics
maPlot.func | Scatter-plots with fitted curves and text
maPrintTip | Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays
maPrintTip,marrayLayout-method | Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays
maPrintTip,marrayNorm-method | Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data
maPrintTip,marrayRaw-method | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
maRb | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
maRb,marrayRaw-method | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
maRb<- | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
maRb<-,marrayRaw,matrix-method | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
maRb<-,marrayRaw,NULL-method | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
maRf | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
maRf,marrayRaw-method | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
maRf<- | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
maRf<-,marrayRaw,matrix-method | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
marrayInfo | Class "marrayInfo", description of target samples or spotted probe sequences
marrayInfo-class | Class "marrayInfo", description of target samples or spotted probe sequences
marrayLayout | Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays
marrayLayout-class | Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays
marrayNorm | Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data
marrayNorm-class | Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data
marrayRaw | Class "marrayRaw", classes and methods for pre-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
maSpotCol | Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays
maSpotCol,marrayLayout-method | Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays
maSpotCol,marrayNorm-method | Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data
maSpotCol,marrayRaw-method | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
maSpotRow | Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays
maSpotRow,marrayLayout-method | Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays
maSpotRow,marrayNorm-method | Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data
maSpotRow,marrayRaw-method | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
maSub | Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays
maSub,marrayLayout-method | Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays
maSub,marrayNorm-method | Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data
maSub,marrayRaw-method | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
maSub<- | Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays
maSub<-,marrayLayout,logical-method | Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays
maSub<-,marrayLayout,numeric-method | Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays
maSub<-,marrayNorm-method | Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data
maSub<-,marrayRaw-method | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
maTargets | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
maTargets,marrayNorm-method | Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data
maTargets,marrayRaw-method | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
maTargets<- | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
maTargets<-,marrayNorm,marrayInfo-method | Class "marrayInfo", description of target samples or spotted probe sequences
maTargets<-,marrayRaw,marrayInfo-method | Class "marrayInfo", description of target samples or spotted probe sequences
maText | Highlight points on a plot
maTop | Identify extreme values
maTwoSamples | Changing signs for two sample analysis
maW | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
maW,marrayNorm-method | Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data
maW,marrayRaw-method | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
maW<- | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
maW<-,marrayNorm,matrix-method | Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data
maW<-,marrayRaw,matrix-method | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
mean.na | Basic Statistical Functions for Handling Missing Values

## -- O --

opVersionID | Determine the operon oligo set ID
order.na | Basic Statistical Functions for Handling Missing Values

## -- P --

plot.gene.cluster | Internal marray functions
plot.marrayNorm | Scatter-plots for cDNA microarray spot statistics
plot.marrayRaw | Scatter-plots for cDNA microarray spot statistics
points,marrayNorm-method | Scatter-plots for cDNA microarray spot statistics
points,marrayRaw-method | Scatter-plots for cDNA microarray spot statistics
print,marrayInfo-method | Class "marrayInfo", description of target samples or spotted probe sequences
print,marrayLayout-method | Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays
print,marrayNorm-method | Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data
print,marrayRaw-method | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
prod.na | Basic Statistical Functions for Handling Missing Values

## -- Q --

quantile.na | Basic Statistical Functions for Handling Missing Values

## -- R --

rbind,marrayInfo-method | Class "marrayInfo", description of target samples or spotted probe sequences
rbind.marrayInfo | Combine marrayRaw, marrayNorm or marrayInfo Objects
read.Agilent | Create objects of class "marrayRaw"
read.fname | Internal marray functions
read.Galfile | Reading GenePix Gal file
read.GenePix | Create objects of class "marrayRaw"
read.marrayInfo | Create objects of class marrayInfo
read.marrayLayout | Create objects of class marrayLayout
read.marrayRaw | Create objects of class "marrayRaw"
read.SMD | Create objects of class "marrayRaw"
read.Spot | Create objects of class "marrayRaw"
rm.na | Remove missing values

## -- S --

scale.na | Basic Statistical Functions for Handling Missing Values
SFGL | Creating URL strings for external database links
show,marrayNorm-method | Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data
show,marrayRaw-method | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
show,ShowLargeObject-method | Show Large Data Object - class
ShowLargeObject-class | Show Large Data Object - class
stat.confband.text | Rank genes according to the value of a statistic.
stat.gene.cluster | Internal marray functions
stat.gnames | Sort Genes According to the Value of a Statistic
sum.na | Basic Statistical Functions for Handling Missing Values
summary,marrayInfo-method | Class "marrayInfo", description of target samples or spotted probe sequences
summary,marrayLayout-method | Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays
summary,marrayNorm-method | Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data
summary,marrayRaw-method | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
summary-methods | Printing summary methods for microarray objects
swirl | Gene expression data from Swirl zebrafish cDNA microarray experiment
swirl.1.spot | Gene expression data from Swirl zebrafish cDNA microarray experiment
swirl.2.spot | Gene expression data from Swirl zebrafish cDNA microarray experiment
swirl.3.spot | Gene expression data from Swirl zebrafish cDNA microarray experiment
swirl.4.spot | Gene expression data from Swirl zebrafish cDNA microarray experiment
SwirlSample | Gene expression data from Swirl zebrafish cDNA microarray experiment
SwirlSample.txt | Gene expression data from Swirl zebrafish cDNA microarray experiment

## -- T --

table2html | Display gene list as a HTML page
tablegen | Internal marray functions
text,marrayNorm-method | Scatter-plots for cDNA microarray spot statistics
text,marrayRaw-method | Scatter-plots for cDNA microarray spot statistics

## -- U --

UCBFGL | Creating URL strings for external database links
URLstring | Creating URL strings for external database links

## -- V --

var.na | Basic Statistical Functions for Handling Missing Values

## -- W --

widget.mapGeneInfo | Creating URL strings for external database links
widget.marrayInfo | Create objects of class marrayInfo
widget.marrayLayout | Create objects of class marrayLayout
widget.marrayRaw | Create objects of class "marrayRaw"
widget.TwoSamples | Changing signs for two sample analysis
write.list | Data Output
write.marray | Data Output
write.xls | Data Output

## -- misc --

[ | Subsetting methods for microarray objects
[,marrayInfo-method | Class "marrayInfo", description of target samples or spotted probe sequences
[,marrayLayout-method | Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays
[,marrayNorm-method | Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data
[,marrayRaw-method | Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
[-methods | Subsetting methods for microarray objects