marray v1.50.0

Exploratory analysis for two-color spotted microarray data

Class definitions for two-color spotted microarray data. Fuctions for data input, diagnostic plots, normalization and quality checking.

Functions in marray

Name Description
checkTargetInfo Verifying the order between intensities matrix and target file information
maCompNormA Weights for composite normalization
maDefaultPar Default graphical parameters for microarray objects
maMAD Stratified MAD calculation
maCoord2Ind Convert grid and spot matrix coordinates to spot indices
ShowLargeObject-class Show Large Data Object - class
marrayInfo-class Class "marrayInfo", description of target samples or spotted probe sequences
stat.confband.text Rank genes according to the value of a statistic.
maCompCoord Generate grid and spot matrix coordinates
mapGeneInfo Creating URL strings for external database links
maColorBar Calibration bar for color images
ma2D Stratified bivariate robust local regression
maCompPlate Generate plate IDs
maTwoSamples Changing signs for two sample analysis
write.marray Data Output
maLoessLines Add smoothed fits to a plot
swirl Gene expression data from Swirl zebrafish cDNA microarray experiment
findID Find ID when given an accession number
maNum2Logic Convert a numeric vector of indices to a logical vector
opVersionID Determine the operon oligo set ID
boxplot Boxplots for cDNA microarray spot statistics
maDotsDefaults Replace graphical default parameters by user supplied parameters
coerce-methods Coerce an object to belong to a given microarray class
maImage.func Color image for cDNA microarray spot statistics
maCompLayout Generate a marrayLayout object
maLoess Stratified univariate robust local regression
plot Scatter-plots for cDNA microarray spot statistics
read.Galfile Reading GenePix Gal file
maNormScale Simple scale normalization function
maTop Identify extreme values
maNorm Simple location and scale normalization function
maLegendLines Add a legend to a plot
maInd2Coord Convert spot indices to grid and spot matrix coordinates
summary-methods Printing summary methods for microarray objects
maDotsMatch Replace default arguments of a function by user supplied values
maNormMed Median location normalization function
Internal functions Internal marray functions
read.marrayRaw Create objects of class "marrayRaw"
read.marrayInfo Create objects of class marrayInfo
maCompInd Generate spot indices
marrayNorm-class Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data
read.marrayLayout Create objects of class marrayLayout
image Color image for cDNA microarray spot statistics
dim Retrieve the Dimensions of an marrayRaw, marrayNorm or marrayInfo Object
maGenControls Generating a vector recording the control status of the spotted probe sequences.
maNormMAD MAD scale normalization function
marrayLayout-class Class "marrayLayout", classes and methods for layout parameters of cDNA microarrays
rm.na Remove missing values
write.xls Data Output
stat.gnames Sort Genes According to the Value of a Statistic
[-methods Subsetting methods for microarray objects
cbind Combine marrayRaw, marrayNorm or marrayInfo Objects
htmlPage Display gene list as a HTML page
na Basic Statistical Functions for Handling Missing Values
maGeneTable Table of spot coordinates and gene names
maMed Stratified median calculation
maNormLoess Intensity dependent location normalization function
maNorm2D 2D spatial location normalization function
maSelectGnames Select genes according to the values of a few different statistics
maImage Color image for cDNA microarray spot statistics
maPlot Scatter-plots for cDNA microarray spot statistics
maNormMain Main function for location and scale normalization of cDNA microarray data
maBoxplot Boxplots for cDNA microarray spot statistics
maPalette Microarray color palette
maText Highlight points on a plot
marrayRaw-class Class "marrayRaw", classes and methods for pre-normalization cDNA microarray intensity data
maPlot.func Scatter-plots with fitted curves and text
write.list Data Output
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Details

Date 2009-08-15
License LGPL
URL http://www.maths.usyd.edu.au/u/jeany/
biocViews Microarray, TwoChannel, Preprocessing
Collate maClasses.R maGet.R maSet.R maPrint.R maSubset.R maBind.R maComp.R maDots.R maInput.R maNorm.R maOutput.R maWidget.R maPlots.R maAnnotate.R maRankGenes.R maSMA.R maSearch.R maWrap.R
LazyLoad yes

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