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

## Documentation for package ‘beadarray’ version 2.2.0

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.
- Package NEWS.

## Help Pages

beadarray-package | The beadarray package: a tool for low-level analysis of Illumina BeadArrays
arrayNames | Deprecated Functions
arrayNames-method | Class "BeadLevelList"
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
beadarrayUsersGuide | View beadarray User's Guide
beadLevelData-class | Class "beadLevelData"
BeadLevelList-class | Class "BeadLevelList"
beadStatusVector | Classify each bead according to its control status
BLData | beadLevelData object from an example experiment
boxplot-method | Class "beadLevelData"
BSData | ExpressionSetIllumina object for the example experiment
calculateDetection | Calculate detection scores
calculateOutlierStats | Outlier distribution stats
checkPlatform | Determine expression chip annotation
checkRegistration | Perform check for misregistered array segments.
combine-method | Combine two objects.
controlProbeDetection | Percentage of beads detected
controlProfile | Control annotation for Illumina expression chips
convertBeadLevelList | Convert a BeadLevelList object into a beadLevelData object
createBeadSummaryData | Deprecated Functions
createTargetsFile | A function to generate a targets file given a directory of Illumina bead-level files
Detection | Class "ExpressionSetIllumina"
Detection-method | Class "ExpressionSetIllumina"
Detection<- | Class "ExpressionSetIllumina"
Detection<--method | Class "ExpressionSetIllumina"
dim-method | Retrieve the dimensions of an object
ExpressionControlData | Control annotation for Illumina expression chips
expressionQCPipeline | Flexible bead-level QC pipeline
ExpressionSetIllumina-class | Class "ExpressionSetIllumina"
exprs-method | Class "ExpressionSetIllumina"
exprs<--method | Class "ExpressionSetIllumina"
generateNeighbours | Generate matrix of neighbouring beads
genericBeadIntensityPlot | Plotting the intensities of selected beads on a section
getAnnotation | Storage of annotation information
getArrayData | Deprecated Functions
getArrayData-method | Class "BeadLevelList"
getBeadData | Get raw data from a beadLevelData object
greenChannelTransform | Functions for transforming the data store in a 'beadLevelData' object for easier visualisation or summarisation.
HULK | HULK - Bead Array Normalization by NEighbourhood Residuals
illuminaBackground | Image processing functions
illuminaChannel-class | Class "illuminaChannel"
illuminaForeground | Image processing functions
illuminaOutlierMethod | Identifier outliers on an array section
illuminaSharpen | Image processing functions
imageplot | imageplot for beadLevelData object
insertBeadData | Add, modify or remove data in a beadLevelData object
insertSectionData | Modify the sectionData slot
logGreenChannelTransform | Functions for transforming the data store in a 'beadLevelData' object for easier visualisation or summarisation.
logRatioTransform | Functions for transforming the data store in a 'beadLevelData' object for easier visualisation or summarisation.
logRedChannelTransform | Functions for transforming the data store in a 'beadLevelData' object for easier visualisation or summarisation.
makeQCTable | Tabulate QC scores
medianBackground | Image processing functions
medianNormalise | Median normalise data in a matrix
nObservations | Class "ExpressionSetIllumina"
nObservations-method | Class "ExpressionSetIllumina"
nObservations<- | Class "ExpressionSetIllumina"
nObservations<--method | Class "ExpressionSetIllumina"
normaliseIllumina | Normalise Illumina expression data
numBeads | Gets the number of beads from a beadLevelData object
numBeads-method | Class "beadLevelData"
outlierplot | Plot outlier locations
plotBeadIntensities | Plotting the intensities of selected beads on a section
plotBeadLocations | Plot bead locations
plotChipLayout | Function to Plot the Layout of an Illumina BeadChip
plotMA | Scatter plots and MA-plots for all specified arrays
plotMAXY | Scatter plots and MA-plots for all specified arrays
plotTIFF | Produce plots of the Illumina tiff images
plotXY | Scatter plots and MA-plots for all specified arrays
poscontPlot | Plot the positive controls
processSwathData | Prepare iScan data for use with beadarray
qcData | Class "ExpressionSetIllumina"
qcData-method | Class "ExpressionSetIllumina"
quickSummary | Create summary values for specified IDs
readBeadSummaryData | Read BeadStudio gene expression output
readIllumina | Read bead-level Illumina data
readLocsFile | Read ".locs" file.
readTIFF | Read the Illumina tiff images
redChannelTransform | Functions for transforming the data store in a 'beadLevelData' object for easier visualisation or summarisation.
removeBeadData | Add, modify or remove data in a beadLevelData object
se.exprs-method | Class "ExpressionSetIllumina"
se.exprs<--method | Class "ExpressionSetIllumina"
sectionNames | Gets the section names from a beadLevelData Object
sectionNames-method | Class "beadLevelData"
setAnnotation | Storage of annotation information
setWeights | Set weights from BASH
show-method | Display object summary
showArrayMask | Show Array Mask
summarize | Create a summarized object
[-method | Class "ExpressionSetIllumina"
[[-method | Class "beadLevelData"