# Quality control and low-level analysis of BeadArrays

## Documentation for package `beadarray' version 1.0.0

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

averagePixels | Read BeadArray information into R
backgroundCorrectBeads | Background Correct a BeadLevelList object
BeadLevelList-class | Red, Green Intensity List - class
BeadSummaryList-class | Stores bead summary data - class
biotin_controls | ProbeIDs of Biotin controls
BLData | BeadLevelList for the example experiment
BSData | BeadSummaryList for the example experiment
calculateBackground | Read BeadArray information into R
calculateForegroundIntensities | Read BeadArray information into R
cbind.BeadLevelList | Combine BeadLevelList or BeadSummaryList Objects
cbind.BeadSummaryList | Combine BeadLevelList or BeadSummaryList Objects
checkRandomness | Test for random distribution of co-ordinates
chitest | Test for random distribution of co-ordinates
coerce,BeadLevelList,exprSet2-method | Red, Green Intensity List - class
createBeadSummaryData | Produce bead averages
cy3_controls | ProbeIDs of cy3 controls
dim.BeadLevelList | Retrieve the Dimensions of an BeadLevelList or BeadSummaryList
dim.BeadSummaryList | Retrieve the Dimensions of an BeadLevelList or BeadSummaryList
dimnames.BeadLevelList | Retrieve the Dimension Names of an BeadLevelList or BeadSummaryList Object
dimnames.BeadSummaryList | Retrieve the Dimension Names of an BeadLevelList or BeadSummaryList Object
displayTIFFImage | Display part of a TIFF Image
findAllOutliers | Find outliers on array
findBeadStatus | Find Outliers
findHighestChis | Find least randomly distributed beads
findHighestSD | Highest standard deviation.
FindIlluminaSpotl | Display part of a TIFF Image
findLowestCounts | Find Lowest bead counts
findMostOutliers | Beads with most outliers
getDimensions | Get dimension of an array
getMeanIntensities | Find Bead Type Averages
getProbeCoords | Find Bead Co-ordinates
getProbeIDs | Get unique ProbeIDs
getProbeIndices | Find Outliers
getProbeIndicesC | Find Outliers
getProbeInfo | Get information for ProbeID
getProbeIntensities | Get Intensites of Beads
getUnregisteredBeads | Finds unregistered beads
histBeadCounts | Plot numbers of each bead
housekeeping_controls | ProbeIDs of housekeeping controls
hs_controls | ProbeIDs of high stringency controls
IdentifyBeads | Display part of a TIFF Image
IdentifyIntensity | Display part of a TIFF Image
labelling_controls | ProbeIDs of housekeeping controls
LargeDataObject-class | Large Data Object - class
length.BeadLevelList | Retrieve the Dimensions of an BeadLevelList or BeadSummaryList
length.BeadSummaryList | Retrieve the Dimensions of an BeadLevelList or BeadSummaryList
ls_controls | ProbeIDs of low stringency controls
matrix.mean | Calculate the mean of a matrix
medianNormalise | Median Normalisation for BeadLevelList objects
neg_controls | ProbeIDs of negative stringency controls
normalizeBetweenArrays | Quantile Normalisation for BeadLevelList objects
other_controls | ProbeIDs of other controls
pairwiseMA | Scatter plots and MA-plots for all specified arrays
panel.MA | Scatter plots and MA-plots for all specified arrays
panel.XY | Scatter plots and MA-plots for all specified arrays
plotArray | Plot outline of hexagonal array
plotBeadIntensities | Plot bead intensities
plotBeadLocations | Show bead locations
plotCluster | Clustering of bead position
plotCoords | Show bead locations
plotDistances | Plot the distances between a set of co-ordinates
plotMA.beads | Show MA plots
plotMAXY | Scatter plots and MA-plots for all specified arrays
plotOnSAM | Show variation between all 96 arrays on a SAM
plotProbeDistances | Plot the distances between a set of beads
plotProbeVariation | Plot variation
plotXY.beads | XY plots for two samples
printHead | Subset BeadLevelList, BeadSummaryList
probeCluster | Clustering of bead position
probeDiagnostics | Diagnostics plot for a bead type
qsplineNormalise | Qsplinw Normalisation for BeadLevelList objects
quantileNormalise | Quantile Normalisation for BeadLevelList objects
rbind.BeadSummaryList | Combine BeadLevelList or BeadSummaryList Objects
read.pgmfile | Read BeadArray information into R
readBeadImages | Read BeadArray information into R
readBeadSummaryData | Read bead summary data information into R
readBeadSummaryTargets | Create targets object
readBeadTargets | Create targets object
readCols | Read bead summary data information into R
readNonXYData | Read BeadArray information into R
readProbeInfo | Read Probe Information
Recenter | Display part of a TIFF Image
removeArrays | Finds unregistered beads
sharpen | Read BeadArray information into R
show,LargeDataObject-method | Large Data Object - class
showTIFF | Display part of a TIFF Image
[.BeadLevelList | Subset BeadLevelList, BeadSummaryList
[.BeadSummaryList | Subset BeadLevelList, BeadSummaryList