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

## Documentation for package ‘beadarray’ version 1.8.0

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

arrayNames | Gets the strip/array names from a BeadLevelList Object
arrayNames,BeadLevelList-method | Class "BeadLevelList"
backgroundCorrect | Background correct a BeadLevelList object
backgroundCorrect,BeadLevelList,character,double,logical-method | Class "BeadLevelList"
backgroundCorrect,BeadLevelList-method | Background correct a BeadLevelList object
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
BLData | BeadLevelList objec from an example experiment
boxplotBeads | Box plot of bead intensities
BSData | ExpressionSetIllumina object for the example experiment
class:ExpressionSetIllumina | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
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
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<-,ExpressionSetIllumina,matrix-method | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
dim,BeadLevelList-method | Class "BeadLevelList"
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.
findAllOutliers | Find outliers on a given strip/array
findBeadStatus | Find Outliers
getArrayData | Get raw data from a BeadLevelList object
getArrayData,BeadLevelList-method | Class "BeadLevelList"
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.
imageplot | imageplot for BeadLevelList object
initialize,BeadLevelList-method | Class "BeadLevelList"
initialize,ExpressionSetIllumina-method | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
medianNormalise | Median normalise data in a matrix
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<-,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"
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
plotXY | XY plots for two samples
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<-,ExpressionSetIllumina,list-method | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
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
readQC | Read Illumina control intensities
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.
show,BeadLevelList-method | Class "BeadLevelList"
show,ExpressionSetIllumina-method | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
[,ExpressionSetIllumina-method | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
[[,BeadLevelList,ANY,missing-method | Class "BeadLevelList"