Exploratory analysis for two-color spotted microarray data

Documentation for package ‘marray’ version 1.24.0

User Guides and Package Vignettes

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