Quality control and low-level analysis of BeadArrays


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Documentation for package `beadarray' version 1.0.0

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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