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marray (version 1.50.0)
Exploratory analysis for two-color spotted microarray data
Description
Class definitions for two-color spotted microarray data. Fuctions for data input, diagnostic plots, normalization and quality checking.
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Version
Version
1.50.0
1.48.0
1.46.0
1.44.0
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Version
1.50.0
License
LGPL
Maintainer
Yee Hwa Jean Yang
Last Published
August 15th, 2009
Functions in marray (1.50.0)
Search functions
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