![[R logo]](../../../doc/html/logo.jpg)
| 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 |