# Quality control and low-level analysis of BeadArrays

## Documentation for package ‘beadarray’ version 1.6.0

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

arrayNames | Gets the 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
backgroundCorrect,BeadLevelList-methods | Background Correct a BeadLevelList object
backgroundNormalise, ExpressionSetIllumina,ExpressionSetIllumina-method | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
backgroundNormalise, ExpressionSetIllumina-methods | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
BeadChipSummary | Interactive bead level plotting
BeadLevelList | Class "BeadLevelList"
BeadLevelList-class | Class "BeadLevelList"
beadResids | Calculates per array bead-level residuals
BLData | BeadLevelList for the 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 a BeadLevelList Object
combineBeadLevelLists,BeadLevelList-method | Class "BeadLevelList"
copyBeadLevelList | Copies a BeadLevelList Object
copyBeadLevelList,BeadLevelList-method | Class "BeadLevelList"
createBeadSummaryData | Produce bead averages
createBeadSummaryData, BeadLevelList-method | Find Outliers
createBeadSummaryData,BeadLevelList-method | 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.
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,ANY-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 array
findAllOutliers, BeadLevelList-method | Find Outliers
findAllOutliers-methods | Find outliers on array
findBeadStatus | Find Outliers
getArrayData | Gets the raw data from a BeadLevelList object
getArrayData,BeadLevelList-method | Class "BeadLevelList"
getProbeIndices | Find Outliers
getProbeIndicesC | Find Outliers
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 BeadArrays object
initialize,BeadLevelList-method | Class "BeadLevelList"
initialize,ExpressionSetIllumina-method | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
LargeDataObject-class | Large Data Object - class
medianNormalise | Median Normalisation for BeadLevelList objects
NoBeads | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
NoBeads,ExpressionSetIllumina-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 density of bead intensities
plotBeadIntensities | Plot bead intensities
plotBeadLocations | Show 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
QC | Illumina quality control data
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.
rankInvariantNormalise | Rank Invariant Normalisation for Bead Summary data
readBeadSummaryData | Read BeadStudio gene expression output
readBGX | Read Illumina bgx file into R
readIllumina | Read BeadArray information into R
readQC | Read Illumina quality control information
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.
show,LargeDataObject-method | Large Data Object - class
[,ExpressionSetIllumina-method | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
[[,BeadLevelList,ANY,missing-method | Class "BeadLevelList"