# Quality assessment and low-level analysis for Illumina BeadArray data

## Documentation for package ‘beadarray’ version 1.14.0

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

A B C D E F G H I L M N O P Q R S V misc

## -- A --

addArrayMask | Array Mask
arrayNames | Gets the strip/array names from a BeadLevelList Object
arrayNames,BeadLevelList-method | Class "BeadLevelList"

## -- B --

backgroundControlPlot | QA measures based on bead-level negative controls
backgroundCorrect | Background correct a BeadLevelList object
backgroundCorrect,BeadLevelList,character,double,logical-method | Class "BeadLevelList"
backgroundCorrect,BeadLevelList-method | Background correct a BeadLevelList object
backgroundCorrect,RGList-method | Background correct a BeadLevelList object
BASH | BASH - BeadArray Subversion of Harshlight
BASHCompact | BASH - Compact Defect Analysis
BASHDiffuse | BASH - Diffuse Defect Analysis
BASHExtended | BASH - Extended Defect Analysis
beadarrayUsersGuide | View beadarray User's Guide
BeadChipSummary | Interactive bead-level plotting
BeadLevelList | Class "BeadLevelList"
BeadLevelList-class | Class "BeadLevelList"
beadResids | Calculates per strip/array bead-level residuals
BGFilter | Background Filter
BGFilterWeighted | Weighted Background Filter
BLData | BeadLevelList objec from an example experiment
boxplotBeads | Box plot of bead intensities
BSData | ExpressionSetIllumina object for the example experiment

## -- C --

calculateBeadLevelScores | Quality assessment for expression chips
calculateDetection | Calculate detection scores
chooseClusters | Choose Clusters
class:ExpressionSetIllumina | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
clearArrayMask | Array Mask
closeImage | Close Image
combine,ExpressionSetIllumina,ANY-method | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
combine,ExpressionSetIllumina,ExpressionSetIllumina-method | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
combineBeadLevelLists | Combines data from two BeadLevelList objects
combineBeadLevelLists,BeadLevelList-method | Class "BeadLevelList"
copyBeadLevelList | Copies a BeadLevelList Object
copyBeadLevelList,BeadLevelList-method | Class "BeadLevelList"
createBeadSummaryData | Produce bead averages

## -- D --

denseRegions | Find Dense Regions of Points (as used in diffuse defect analysis).
Detection | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
Detection,ExpressionSetIllumina-method | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
Detection<- | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
Detection<-,ExpressionSetIllumina,matrix-method | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
dim,BeadLevelList-method | Class "BeadLevelList"

## -- E --

ExpressionControlData | Control annotation for Illumina expression chips
ExpressionSetIllumina-class | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
exprs,ExpressionSetIllumina-method | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
exprs<-,ExpressionSetIllumina,matrix-method | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.

## -- F --

findAllOutliers | Find outliers on a given strip/array
findBeadStatus | Find Outliers

## -- G --

generateE | Generate Error Image for BeadLevelList object
generateNeighbours | Generate Neighbours Matrix for BeadLevelList object
getAnnotation | Storage of annotation information for Illumina expression chips
getArrayData | Get raw data from a BeadLevelList object
getArrayData,BeadLevelList-method | Class "BeadLevelList"
getControlAnno | Storage of annotation information for Illumina expression chips
getProbeIntensities | Find Outliers
getProbeIntensities,BeadLevelList-method | Find Outliers
getVariance | Gets the bead-type variances from an ExpressionSetIllumina Object
getVariance,ExpressionSetIllumina-method | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
gradientPlot | Quality assessment for expression chips

## -- H --

HULK | HULK - Bead Array Normalization by NEighbourhood Residuals
HULKResids | HULK - Residuals

## -- I --

imageplot | imageplot for BeadLevelList object
initialize,BeadLevelList-method | Class "BeadLevelList"
initialize,ExpressionSetIllumina-method | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.

## -- L --

lmhPlot | Plot the bead-level hybridisation controls

## -- M --

medianNormalise | Median normalise data in a matrix

## -- N --

NoBeads | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
NoBeads,ExpressionSetIllumina-method | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
NoBeads<- | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
NoBeads<-,ExpressionSetIllumina,matrix-method | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
normaliseIllumina | Normalise Illumina expression data
numBeads | Gets the number of beads from a BeadLevelList object
numBeads,BeadLevelList-method | Class "BeadLevelList"

## -- O --

outlierPlot | Locations of outliers on an Illumina chip

## -- P --

pData,BeadLevelList-method | Class "BeadLevelList"
phenoData,BeadLevelList-method | Class "BeadLevelList"
plotBeadDensities | plot densities of bead intensities
plotBeadIntensities | Plot bead intensities
plotBeadLocations | Plot bead locations
plotMA | Show MA plots
plotMAXY | Scatter plots and MA-plots for all specified arrays
plotOnSAM | Show variation between all 96 arrays
plotRG | Plot bead-level data: R vs G intensities
plotTIFF | Produce plots of the Illumina tiff images
plotXY | XY plots for two samples
poscontPlot | Plot bead-level housekeeping and biotin controls
probePairsPlot | QA plot using perfect match and mismatch controls

## -- Q --

qcBeadLevel | Generate simple diagnostic plots for Illumina bead-level data
QCInfo | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
QCInfo,ExpressionSetIllumina-method | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
QCInfo<- | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
QCInfo<-,ExpressionSetIllumina,list-method | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.

## -- R --

rankInvariantNormalise | Rank Invariant normalise data in a matrix
readBeadSummaryData | Read BeadStudio gene expression output
readBGX | Read Illumina .bgx file into R
readIllumina | Read bead-level data into R
readLocs | Read the .locs file produced with each array
readQC | Read Illumina control intensities
readTIFF | Read the Illumina tiff images
removeArrayMask | Array Mask

## -- S --

SAMSummary | Interactive bead-level plotting
se.exprs,ExpressionSetIllumina-method | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
se.exprs<-,ExpressionSetIllumina,matrix-method | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
setAnnotation | Storage of annotation information for Illumina expression chips
setWeights | Set BeadLevelList Weights
show,BeadLevelList-method | Class "BeadLevelList"
show,ExpressionSetIllumina-method | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
showArrayMask | Array Mask

## -- V --

viewBeads | View Beads

## -- misc --

[,ExpressionSetIllumina-method | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
[[,BeadLevelList,ANY,missing-method | Class "BeadLevelList"