# Exploratory analysis for two-color spotted microarray data

## Documentation for package ‘marray’ version 1.28.0

- DESCRIPTION file.
- Overview of user guides and package vignettes; 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-method | Boxplots for cDNA microarray spot statistics

## -- C --

cbind-method | Class "marrayNorm", classes and methods for post-normalization cDNA
cbind-method | Class "marrayRaw", classes and methods for pre-normalization cDNA
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
coerce | Coerce an object to belong to a given microarray class
coerce-method | Class "marrayNorm", classes and methods for post-normalization cDNA
coerce-methods | Coerce an object to belong to a given microarray class
controlCode | Generating a vector recording the control status of the spotted probe
cor.na | Basic Statistical Functions for Handling Missing Values

## -- D --

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

## -- 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-method | Color image for cDNA microarray spot statistics

## -- L --

length.na | Basic Statistical Functions for Handling Missing Values
lines-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
maA-method | Class "marrayNorm", classes and methods for post-normalization cDNA
maA-method | Class "marrayRaw", classes and methods for pre-normalization cDNA
maA<- | Class "marrayNorm", classes and methods for post-normalization cDNA
maA<--method | Class "marrayNorm", classes and methods for post-normalization cDNA
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
maControls-method | Class "marrayLayout", classes and methods for layout parameters of cDNA
maControls-method | Class "marrayNorm", classes and methods for post-normalization cDNA
maControls-method | Class "marrayRaw", classes and methods for pre-normalization cDNA
maControls<- | Class "marrayLayout", classes and methods for layout parameters of cDNA
maControls<--method | Class "marrayLayout", classes and methods for layout parameters of cDNA
maControls<--method | Class "marrayNorm", classes and methods for post-normalization cDNA
maControls<--method | Class "marrayRaw", classes and methods for pre-normalization cDNA
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
maGb-method | Class "marrayRaw", classes and methods for pre-normalization cDNA
maGb<- | Class "marrayRaw", classes and methods for pre-normalization cDNA
maGb<--method | Class "marrayRaw", classes and methods for pre-normalization cDNA
maGenControls | Generating a vector recording the control status of the spotted probe
maGeneTable | Table of spot coordinates and gene names
maGf | Class "marrayRaw", classes and methods for pre-normalization cDNA
maGf-method | Class "marrayRaw", classes and methods for pre-normalization cDNA
maGf<- | Class "marrayRaw", classes and methods for pre-normalization cDNA
maGf<--method | Class "marrayRaw", classes and methods for pre-normalization cDNA
maGnames | Class "marrayRaw", classes and methods for pre-normalization cDNA
maGnames-method | Class "marrayNorm", classes and methods for post-normalization cDNA
maGnames-method | Class "marrayRaw", classes and methods for pre-normalization cDNA
maGnames<- | Class "marrayRaw", classes and methods for pre-normalization cDNA
maGnames<--method | Class "marrayInfo", description of target samples or spotted probe
maGridCol | Class "marrayLayout", classes and methods for layout parameters of cDNA
maGridCol-method | Class "marrayLayout", classes and methods for layout parameters of cDNA
maGridCol-method | Class "marrayNorm", classes and methods for post-normalization cDNA
maGridCol-method | Class "marrayRaw", classes and methods for pre-normalization cDNA
maGridRow | Class "marrayLayout", classes and methods for layout parameters of cDNA
maGridRow-method | Class "marrayLayout", classes and methods for layout parameters of cDNA
maGridRow-method | Class "marrayNorm", classes and methods for post-normalization cDNA
maGridRow-method | Class "marrayRaw", classes and methods for pre-normalization cDNA
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
maInfo-method | Class "marrayInfo", description of target samples or spotted probe
maInfo<- | Class "marrayInfo", description of target samples or spotted probe
maInfo<--method | Class "marrayInfo", description of target samples or spotted probe
maLabels | Class "marrayInfo", description of target samples or spotted probe
maLabels-method | Class "marrayInfo", description of target samples or spotted probe
maLabels<- | Class "marrayInfo", description of target samples or spotted probe
maLabels<--method | Class "marrayInfo", description of target samples or spotted probe
maLayout | Class "marrayRaw", classes and methods for pre-normalization cDNA
maLayout-method | Class "marrayNorm", classes and methods for post-normalization cDNA
maLayout-method | Class "marrayRaw", classes and methods for pre-normalization cDNA
maLayout<- | Class "marrayRaw", classes and methods for pre-normalization cDNA
maLayout<--method | Class "marrayLayout", classes and methods for layout parameters of cDNA
maLegendLines | Add a legend to a plot
maLG | Class "marrayRaw", classes and methods for pre-normalization cDNA
maLG-method | Class "marrayNorm", classes and methods for post-normalization cDNA
maLG-method | Class "marrayRaw", classes and methods for pre-normalization cDNA
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
maLR-method | Class "marrayNorm", classes and methods for post-normalization cDNA
maLR-method | Class "marrayRaw", classes and methods for pre-normalization cDNA
maM | Class "marrayNorm", classes and methods for post-normalization cDNA
maM-method | Class "marrayNorm", classes and methods for post-normalization cDNA
maM-method | Class "marrayRaw", classes and methods for pre-normalization cDNA
maM<- | Class "marrayNorm", classes and methods for post-normalization cDNA
maM<--method | Class "marrayNorm", classes and methods for post-normalization cDNA
maMAD | Stratified MAD calculation
maMed | Stratified median calculation
maMloc | Class "marrayNorm", classes and methods for post-normalization cDNA
maMloc-method | Class "marrayNorm", classes and methods for post-normalization cDNA
maMloc<- | Class "marrayNorm", classes and methods for post-normalization cDNA
maMloc<--method | Class "marrayNorm", classes and methods for post-normalization cDNA
maMscale | Class "marrayNorm", classes and methods for post-normalization cDNA
maMscale-method | Class "marrayNorm", classes and methods for post-normalization cDNA
maMscale<- | Class "marrayNorm", classes and methods for post-normalization cDNA
maMscale<--method | Class "marrayNorm", classes and methods for post-normalization cDNA
maNgc | Class "marrayLayout", classes and methods for layout parameters of cDNA
maNgc-method | Class "marrayLayout", classes and methods for layout parameters of cDNA
maNgc-method | Class "marrayNorm", classes and methods for post-normalization cDNA
maNgc-method | Class "marrayRaw", classes and methods for pre-normalization cDNA
maNgc<- | Class "marrayLayout", classes and methods for layout parameters of cDNA
maNgc<--method | Class "marrayLayout", classes and methods for layout parameters of cDNA
maNgc<--method | Class "marrayNorm", classes and methods for post-normalization cDNA
maNgc<--method | Class "marrayRaw", classes and methods for pre-normalization cDNA
maNgr | Class "marrayLayout", classes and methods for layout parameters of cDNA
maNgr-method | Class "marrayLayout", classes and methods for layout parameters of cDNA
maNgr-method | Class "marrayNorm", classes and methods for post-normalization cDNA
maNgr-method | Class "marrayRaw", classes and methods for pre-normalization cDNA
maNgr<- | Class "marrayLayout", classes and methods for layout parameters of cDNA
maNgr<--method | Class "marrayLayout", classes and methods for layout parameters of cDNA
maNgr<--method | Class "marrayNorm", classes and methods for post-normalization cDNA
maNgr<--method | Class "marrayRaw", classes and methods for pre-normalization cDNA
maNorm | Simple location and scale normalization function
maNorm2D | 2D spatial location normalization function
maNormCall | Class "marrayNorm", classes and methods for post-normalization cDNA
maNormCall-method | Class "marrayNorm", classes and methods for post-normalization cDNA
maNormLoess | Intensity dependent location normalization function
maNormMAD | MAD scale normalization function
maNormMain | Main function for location and scale normalization of cDNA microarray
maNormMed | Median location normalization function
maNormScale | Simple scale normalization function
maNotes | Class "marrayInfo", description of target samples or spotted probe
maNotes-method | Class "marrayInfo", description of target samples or spotted probe
maNotes-method | Class "marrayLayout", classes and methods for layout parameters of cDNA
maNotes-method | Class "marrayNorm", classes and methods for post-normalization cDNA
maNotes-method | Class "marrayRaw", classes and methods for pre-normalization cDNA
maNotes<- | Class "marrayInfo", description of target samples or spotted probe
maNotes<--method | Class "marrayInfo", description of target samples or spotted probe
maNotes<--method | Class "marrayLayout", classes and methods for layout parameters of cDNA
maNotes<--method | Class "marrayNorm", classes and methods for post-normalization cDNA
maNotes<--method | Class "marrayRaw", classes and methods for pre-normalization cDNA
maNsamples | Class "marrayRaw", classes and methods for pre-normalization cDNA
maNsamples-method | Class "marrayNorm", classes and methods for post-normalization cDNA
maNsamples-method | Class "marrayRaw", classes and methods for pre-normalization cDNA
maNsc | Class "marrayLayout", classes and methods for layout parameters of cDNA
maNsc-method | Class "marrayLayout", classes and methods for layout parameters of cDNA
maNsc-method | Class "marrayNorm", classes and methods for post-normalization cDNA
maNsc-method | Class "marrayRaw", classes and methods for pre-normalization cDNA
maNsc<- | Class "marrayLayout", classes and methods for layout parameters of cDNA
maNsc<--method | Class "marrayLayout", classes and methods for layout parameters of cDNA
maNsc<--method | Class "marrayNorm", classes and methods for post-normalization cDNA
maNsc<--method | Class "marrayRaw", classes and methods for pre-normalization cDNA
maNspots | Class "marrayLayout", classes and methods for layout parameters of cDNA
maNspots-method | Class "marrayLayout", classes and methods for layout parameters of cDNA
maNspots-method | Class "marrayNorm", classes and methods for post-normalization cDNA
maNspots-method | Class "marrayRaw", classes and methods for pre-normalization cDNA
maNspots<- | Class "marrayLayout", classes and methods for layout parameters of cDNA
maNspots<--method | Class "marrayLayout", classes and methods for layout parameters of cDNA
maNspots<--method | Class "marrayNorm", classes and methods for post-normalization cDNA
maNspots<--method | Class "marrayRaw", classes and methods for pre-normalization cDNA
maNsr | Class "marrayLayout", classes and methods for layout parameters of cDNA
maNsr-method | Class "marrayLayout", classes and methods for layout parameters of cDNA
maNsr-method | Class "marrayNorm", classes and methods for post-normalization cDNA
maNsr-method | Class "marrayRaw", classes and methods for pre-normalization cDNA
maNsr<- | Class "marrayLayout", classes and methods for layout parameters of cDNA
maNsr<--method | Class "marrayLayout", classes and methods for layout parameters of cDNA
maNsr<--method | Class "marrayNorm", classes and methods for post-normalization cDNA
maNsr<--method | Class "marrayRaw", classes and methods for pre-normalization cDNA
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
maPlate-method | Class "marrayLayout", classes and methods for layout parameters of cDNA
maPlate-method | Class "marrayNorm", classes and methods for post-normalization cDNA
maPlate-method | Class "marrayRaw", classes and methods for pre-normalization cDNA
maPlate<- | Class "marrayLayout", classes and methods for layout parameters of cDNA
maPlate<--method | Class "marrayLayout", classes and methods for layout parameters of cDNA
maPlate<--method | Class "marrayNorm", classes and methods for post-normalization cDNA
maPlate<--method | Class "marrayRaw", classes and methods for pre-normalization cDNA
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
maPrintTip-method | Class "marrayLayout", classes and methods for layout parameters of cDNA
maPrintTip-method | Class "marrayNorm", classes and methods for post-normalization cDNA
maPrintTip-method | Class "marrayRaw", classes and methods for pre-normalization cDNA
maRb | Class "marrayRaw", classes and methods for pre-normalization cDNA
maRb-method | Class "marrayRaw", classes and methods for pre-normalization cDNA
maRb<- | Class "marrayRaw", classes and methods for pre-normalization cDNA
maRb<--method | Class "marrayRaw", classes and methods for pre-normalization cDNA
maRf | Class "marrayRaw", classes and methods for pre-normalization cDNA
maRf-method | Class "marrayRaw", classes and methods for pre-normalization cDNA
maRf<- | Class "marrayRaw", classes and methods for pre-normalization cDNA
maRf<--method | Class "marrayRaw", classes and methods for pre-normalization cDNA
marrayInfo | Class "marrayInfo", description of target samples or spotted probe
marrayInfo-class | Class "marrayInfo", description of target samples or spotted probe
marrayLayout | Class "marrayLayout", classes and methods for layout parameters of cDNA
marrayLayout-class | Class "marrayLayout", classes and methods for layout parameters of cDNA
marrayNorm | Class "marrayNorm", classes and methods for post-normalization cDNA
marrayNorm-class | Class "marrayNorm", classes and methods for post-normalization cDNA
marrayRaw | Class "marrayRaw", classes and methods for pre-normalization cDNA
marrayRaw-class | Class "marrayRaw", classes and methods for pre-normalization cDNA
maSelectGnames | Select genes according to the values of a few different statistics
maSpotCol | Class "marrayLayout", classes and methods for layout parameters of cDNA
maSpotCol-method | Class "marrayLayout", classes and methods for layout parameters of cDNA
maSpotCol-method | Class "marrayNorm", classes and methods for post-normalization cDNA
maSpotCol-method | Class "marrayRaw", classes and methods for pre-normalization cDNA
maSpotRow | Class "marrayLayout", classes and methods for layout parameters of cDNA
maSpotRow-method | Class "marrayLayout", classes and methods for layout parameters of cDNA
maSpotRow-method | Class "marrayNorm", classes and methods for post-normalization cDNA
maSpotRow-method | Class "marrayRaw", classes and methods for pre-normalization cDNA
maSub | Class "marrayLayout", classes and methods for layout parameters of cDNA
maSub-method | Class "marrayLayout", classes and methods for layout parameters of cDNA
maSub-method | Class "marrayNorm", classes and methods for post-normalization cDNA
maSub-method | Class "marrayRaw", classes and methods for pre-normalization cDNA
maSub<- | Class "marrayLayout", classes and methods for layout parameters of cDNA
maSub<--method | Class "marrayLayout", classes and methods for layout parameters of cDNA
maSub<--method | Class "marrayNorm", classes and methods for post-normalization cDNA
maSub<--method | Class "marrayRaw", classes and methods for pre-normalization cDNA
maTargets | Class "marrayRaw", classes and methods for pre-normalization cDNA
maTargets-method | Class "marrayNorm", classes and methods for post-normalization cDNA
maTargets-method | Class "marrayRaw", classes and methods for pre-normalization cDNA
maTargets<- | Class "marrayRaw", classes and methods for pre-normalization cDNA
maTargets<--method | Class "marrayInfo", description of target samples or spotted probe
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
maW-method | Class "marrayNorm", classes and methods for post-normalization cDNA
maW-method | Class "marrayRaw", classes and methods for pre-normalization cDNA
maW<- | Class "marrayRaw", classes and methods for pre-normalization cDNA
maW<--method | Class "marrayNorm", classes and methods for post-normalization cDNA
maW<--method | Class "marrayRaw", classes and methods for pre-normalization cDNA
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-method | Scatter-plots for cDNA microarray spot statistics
print-method | Class "marrayInfo", description of target samples or spotted probe
print-method | Class "marrayLayout", classes and methods for layout parameters of cDNA
print-method | Class "marrayNorm", classes and methods for post-normalization cDNA
print-method | Class "marrayRaw", classes and methods for pre-normalization cDNA
prod.na | Basic Statistical Functions for Handling Missing Values

## -- Q --

quantile.na | Basic Statistical Functions for Handling Missing Values

## -- R --

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