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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

License

LGPL

Maintainer

Yee Hwa Jean Yang

Last Published

February 15th, 2017

Functions in marray (1.50.0)

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