beadarray: Quality assessment and low-level analysis for Illumina BeadArray data

The package is able to read bead-level data (raw TIFFs and text files) output by BeadScan as well as bead-summary data from BeadStudio. Methods for quality assessment and low-level analysis are provided.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("beadarray")
AuthorMark Dunning, Mike Smith, Jonathan Cairns, Andy Lynch, Matt Ritchie
Bioconductor views Microarray OneChannel Preprocessing QualityControl
Date of publicationNone
MaintainerMark Dunning <Mark.Dunning@cruk.cam.ac.uk>
LicenseGPL-2
Version2.24.0

View on Bioconductor

Man pages

addFeatureData: Add probe data

annotationInterface: Storage of annotation information

backgroundCorrectSingleSection: Background correct an array-section

BASH: BASH - BeadArray Subversion of Harshlight

BASHCompact: BASH - Compact Defect Analysis

BASHDiffuse: BASH - Diffuse Defect Analysis

BASHExtended: BASH - Extended Defect Analysis

beadarray-package: The beadarray package: a tool for low-level analysis of...

beadarrayUsersGuide: View beadarray User's Guide

boxplot: Boxplots from summary data

calculateDetection: Calculate detection scores

calculateOutlierStats: Outlier distribution stats

checkRegistration: Perform check for misregistered array segments.

class-beadLevelData: Class "beadLevelData"

class-BeadLevelList: Class "BeadLevelList"

class-beadRegistrationData: Class "beadRegistrationData"

class-ExpressionSetIllumina: Class "ExpressionSetIllumina"

class-illuminaChannel: Class "illuminaChannel"

class-limmaResults: Class "limmaResults"

combine: Combine two objects.

controlProbeDetection: Percentage of beads detected

convertBeadLevelList: Convert a BeadLevelList object into a beadLevelData object

createTargetsFile: A function to generate a targets file given a directory of...

deprecatedFunctions: Deprecated Functions

dim: Retrieve the dimensions of an object

expressionQCPipeline: Flexible bead-level QC pipeline

generateNeighbours: Generate matrix of neighbouring beads

GEO: Create files for a Gene Expression Omnibus submission

GEOtemplate: GEO required fields

getBeadData: Get raw data from a beadLevelData object

HULK: HULK - Bead Array Normalization by NEighbourhood Residuals

identifyControlBeads: Classify each bead according to its control status

illuminaOutlierMethod: Identifier outliers on an array section

imageplot: imageplot for beadLevelData object

imageProcessing: Image processing functions

insertBeadData: Add, modify or remove data in a beadLevelData object

insertSectionData: Modify the sectionData slot

limmaDE: Differential expression using limma

makeControlProfile: Retrieve control beads

makeQCTable: Tabulate QC scores

maplots: Function to construct the classic MA plots from a dataset

medianNormalise: Median normalise data in a matrix

metrics: Accessing metrics information in bead-level objects

noOutlierMethod: returns no outliers on an array section

normaliseIllumina: Normalise Illumina expression data

numBeads: Gets the number of beads from a beadLevelData object

outlierplot: Plot outlier locations

platformSigs: Annotation definitions

plotBeadIntensities: Plotting the intensities of selected beads on a section

plotBeadLocations: Plot bead locations

plotChipLayout: Function to Plot the Layout of an Illumina BeadChip

plotMAXY: Scatter plots and MA-plots for all specified arrays

plotTIFF: Produce plots of the Illumina tiff images

poscontPlot: Plot the positive controls

processSwathData: Prepare iScan data for use with beadarray

quickSummary: Create summary values for specified IDs

readBeadSummaryData: Read BeadStudio gene expression output

readIdatFiles: Read BeadScan gene expression output

readIllumina: Read bead-level Illumina data

readLocsFile: Read ".locs" file.

readTIFF: Read the Illumina tiff images

sampleSheet: Read a Sample sheet for a BeadArray experiment

sectionNames: Gets the section names from a beadLevelData Object

setWeights: Set weights from BASH

show: Display object summary

showArrayMask: Show Array Mask

squeezedVarOutlierMethod: Identifier outliers on an array section

summarize: Create a summarized object

transformationFunctions: Functions for transforming the data store in a...

weightsOutlierMethod: returns all beads with weight=0.

Functions

addFeatureData Man page
annotation Man page
annotation<-,beadLevelData,character-method Man page
annotation,beadLevelData-method Man page
annotation<-,ExpressionSetIllumina,character-method Man page
annotation,ExpressionSetIllumina-method Man page
arrayNames Man page
arrayNames,BeadLevelList-method Man page
ArrayWeights Man page
ArrayWeights<- Man page
ArrayWeights,limmaResults-method Man page
ArrayWeights<-,limmaResults,numeric-method Man page
backgroundCorrectSingleSection Man page
BASH Man page
BASHCompact Man page
BASHDiffuse Man page
BASHExtended Man page
beadarray-package Man page
beadarrayUsersGuide Man page
[[,beadLevelData,ANY,missing-method Man page
beadLevelData-class Man page
BeadLevelList Man page
BeadLevelList-class Man page
beadRegistrationData-class Man page
beadStatusVector Man page
boxplot,beadLevelData-method Man page
boxplot,beadRegistrationData-method Man page
boxplot,ExpressionSetIllumina-method Man page
calculateDetection Man page
calculateOutlierStats Man page
checkPlatform Man page
checkRegistration Man page
combine,beadLevelData,beadLevelData-method Man page
combinedControlPlot Man page
combine,ExpressionSetIllumina,ExpressionSetIllumina-method Man page
combine,limmaResults,limmaResults-method Man page
ContrastMatrix Man page
ContrastMatrix<- Man page
ContrastMatrix<-,limmaResults,matrix-method Man page
ContrastMatrix,limmaResults-method Man page
controlProbeDetection Man page
convertBeadLevelList Man page
createBeadSummaryData Man page
createGEOMatrix Man page
createGEOMeta Man page
createTargetsFile Man page
DesignMatrix Man page
DesignMatrix<- Man page
DesignMatrix<-,limmaResults,matrix-method Man page
DesignMatrix,limmaResults-method Man page
Detection Man page
Detection<- Man page
Detection<-,ExpressionSetIllumina,matrix-method Man page
Detection,ExpressionSetIllumina-method Man page
dim,beadLevelData-method Man page
dim,ExpressionSetIllumina-method Man page
dim,limmaResults-method Man page
expressionQCPipeline Man page
[,ExpressionSetIllumina,ANY-method Man page
ExpressionSetIllumina-class Man page
[,ExpressionSetIllumina-method Man page
exprs<-,ExpressionSetIllumina,matrix-method Man page
exprs,ExpressionSetIllumina-method Man page
generateNeighbours Man page
genericBeadIntensityPlot Man page
getAnnotation Man page
getArrayData Man page
getArrayData,BeadLevelList-method Man page
getBeadData Man page
getControlProfile Man page
greenChannel Man page
greenChannelTransform Man page
HULK Man page
identifyControlBeads Man page
illuminaBackground Man page
illuminaChannel-class Man page
illuminaForeground Man page
illuminaOutlierMethod Man page
illuminaSharpen Man page
imageplot Man page
insertBeadData Man page
insertSectionData Man page
limmaDE Man page
limmaResults-class Man page
[,limmaResults-method Man page
LogFC Man page
LogFC<- Man page
LogFC<-,limmaResults,matrix-method Man page
LogFC,limmaResults-method Man page
logGreenChannelTransform Man page
LogOdds Man page
LogOdds<- Man page
LogOdds<-,limmaResults,matrix-method Man page
LogOdds,limmaResults-method Man page
logRatioTransform Man page
logRedChannelTransform Man page
makeControlProfile Man page
makeGEOSubmissionFiles Man page
makeQCTable Man page
medianBackground Man page
medianNormalise Man page
metaTemplate Man page
metrics Man page
metrics,beadLevelData-method Man page
nObservations Man page
nObservations<- Man page
nObservations<-,ExpressionSetIllumina,matrix-method Man page
nObservations,ExpressionSetIllumina-method Man page
noOutlierMethod Man page
normaliseIllumina Man page
numBeads Man page
numBeads,beadLevelData-method Man page
outlierplot Man page
p95 Man page
p95,beadLevelData,character-method Man page
platformSigs Man page
plotBeadIntensities Man page
plotBeadLocations Man page
plotChipLayout Man page
plot,limmaResults-method Man page
plotMA Man page
plotMA,ExpressionSetIllumina-method Man page
plotMAXY Man page
plotTIFF Man page
plotXY Man page
poscontPlot Man page
processSwathData Man page
PValue Man page
PValue<- Man page
PValue<-,limmaResults,matrix-method Man page
PValue,limmaResults-method Man page
qcData Man page
qcData,ExpressionSetIllumina-method Man page
quickSummary Man page
readBeadSummaryData Man page
readIdatFiles Man page
readIllumina Man page
readLocsFile Man page
readSampleSheet Man page
readTIFF Man page
redChannelTransform Man page
removeBeadData Man page
sampleSheet Man page
sampleSheet<- Man page
sampleSheet<-,beadLevelData,data.frame-method Man page
sampleSheet,beadLevelData-method Man page
sampleSheet<-,ExpressionSetIllumina,data.frame-method Man page
sampleSheet,ExpressionSetIllumina-method Man page
sectionNames Man page
sectionNames,beadLevelData-method Man page
se.exprs<-,ExpressionSetIllumina,matrix-method Man page
se.exprs,ExpressionSetIllumina-method Man page
setAnnotation Man page
setWeights Man page
showArrayMask Man page
show,beadLevelData-method Man page
show,beadRegistrationData-method Man page
show,ExpressionSetIllumina-method Man page
show,limmaResults-method Man page
snr Man page
snr,beadLevelData,character-method Man page
squeezedVarOutlierMethod Man page
suggestAnnotation Man page
summarize Man page
weightsOutlierMethod Man page

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R R/BASH.R R/ExpressionSetIlluminaNormalisation.R R/ExpressionSetIlluminaPlotting.R R/ExpressionSetIllumina_calculateDetection.R R/GEO.R R/HULK.R R/analyseDirectory.R R/annotation.R R/appendHistory.R R/beadLevelData_QC.R R/beadLevelData_[[.R R/beadLevelData_assignSegments.R R/beadLevelData_backgroundCorrect.R R/beadLevelData_combine.R R/beadLevelData_combinedQCPlot.R R/beadLevelData_dim.R R/beadLevelData_expressionQCPipeline.R R/beadLevelData_getBeadData.R R/beadLevelData_metrics.R R/beadLevelData_numBeads.R R/beadLevelData_outlierPlot.R R/beadLevelData_plotBeadLocations.R R/beadLevelData_sectionData.R R/beadLevelData_sectionNames.R R/beadLevelData_setWeights.R R/beadLevelData_show.R R/beadLevelData_showArrayMask.R R/beadLevelData_spatialPlot.R R/beadLevelData_summarize.R R/beadLevelData_uniqueProbeList.R R/boxplot.R R/checkRegistration.R R/convertBeadLevelList.R R/createTargetsFile.R R/experimental.R R/expressionSetIllumina_channel.R R/expressionSetIllumina_channelNames.R R/getnextXMLtoken.R R/gridPositionsFromLocs.R R/illuminaChannel_initialize.R R/imageProcessing.R R/imageplot.R R/insertBeadData.R R/limmaDE.R R/methods-ExpressionSetIllumina.R R/methods-beadRegistrationData.R R/methods-limmaResults.R R/miscFunctions.R R/nearNonDecodedRegion.R R/obtainLocs.R R/outlierMethods.R R/plotChipLayout.R R/plotTIFF.R R/readBeadLevelTextFile.R R/readBeadSummaryData.R R/readIdatFiles.R R/readIllumina.R R/readLocsFile.R R/readSampleSheet.R R/readTIFF.R R/reports.R R/sampleSheet.R R/simpleXMLparse.R R/standardIlluminaChannels.R R/swathData_assignToImage.R R/swathData_checkSwathStatus.R R/swathData_genSwaths.R R/swathData_processData.R R/swathData_singleBeadIntensity.R R/swathData_writeFiles.R R/zzz.R
build
build/vignette.rds
data
data/datalist
data/metaTemplate.rda
data/platformSigs.rda
inst
inst/CITATION
inst/NEWS
inst/doc
inst/doc/ImageProcessing.R
inst/doc/ImageProcessing.pdf
inst/doc/ImageProcessing.rnw
inst/doc/beadarray.R
inst/doc/beadarray.pdf
inst/doc/beadarray.rnw
inst/doc/beadlevel.R
inst/doc/beadlevel.pdf
inst/doc/beadlevel.rnw
inst/doc/beadsummary.R
inst/doc/beadsummary.pdf
inst/doc/beadsummary.rnw
man
man/BASH.Rd man/BASHCompact.Rd man/BASHDiffuse.Rd man/BASHExtended.Rd man/GEO.Rd man/GEOtemplate.Rd man/HULK.Rd man/addFeatureData.Rd man/annotationInterface.Rd man/backgroundCorrectSingleSection.Rd man/beadarray-package.Rd man/beadarrayUsersGuide.Rd man/boxplot.Rd man/calculateDetection.Rd man/calculateOutlierStats.Rd man/checkRegistration.Rd man/class-BeadLevelList.Rd man/class-ExpressionSetIllumina.Rd man/class-beadLevelData.Rd man/class-beadRegistrationData.Rd man/class-illuminaChannel.Rd man/class-limmaResults.Rd man/combine.Rd man/controlProbeDetection.Rd man/convertBeadLevelList.Rd man/createTargetsFile.Rd man/deprecatedFunctions.Rd man/dim.Rd man/expressionQCPipeline.Rd man/generateNeighbours.Rd man/getBeadData.Rd man/identifyControlBeads.Rd man/illuminaOutlierMethod.Rd man/imageProcessing.Rd man/imageplot.Rd man/insertBeadData.Rd man/insertSectionData.Rd man/limmaDE.Rd man/makeControlProfile.Rd man/makeQCTable.Rd man/maplots.Rd man/medianNormalise.Rd man/metrics.Rd man/noOutlierMethod.Rd man/normaliseIllumina.Rd man/numBeads.Rd man/outlierplot.Rd man/platformSigs.Rd man/plotBeadIntensities.Rd man/plotBeadLocations.Rd man/plotChipLayout.Rd man/plotMAXY.Rd man/plotTIFF.Rd man/poscontPlot.Rd man/processSwathData.Rd man/quickSummary.Rd man/readBeadSummaryData.Rd man/readIdatFiles.Rd man/readIllumina.Rd man/readLocsFile.Rd man/readTIFF.Rd man/sampleSheet.Rd man/sectionNames.Rd man/setWeights.Rd man/show.Rd man/showArrayMask.Rd man/squeezedVarOutlierMethod.Rd man/summarize.Rd man/transformationFunctions.Rd man/weightsOutlierMethod.Rd
src
src/BASH.c
src/HULK.c
src/beadarray.h
src/determiningGridPositions.c
src/findAllOutliers.c
src/imageProcessing.c
vignettes
vignettes/ImageProcessing.rnw
vignettes/beadarray.bib
vignettes/beadarray.rnw
vignettes/beadlevel.rnw
vignettes/beadsummary.rnw

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