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 |