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| 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 "beadLevelData" |
| beadLevelData-class | Class "beadLevelData" |
| BeadLevelList | Class "BeadLevelList" |
| 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 |
| checkRegistration | Perform check for misregistered array segments. |
| combine-method | Class "ExpressionSetIllumina" |
| combine-method | Class "beadLevelData" |
| 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 | Class "ExpressionSetIllumina" |
| dim-method | Class "beadLevelData" |
| ExpressionControlData | Control annotation for Illumina expression chips |
| expressionQCPipeline | Flexible bead-level QC pipeline |
| ExpressionSetIllumina-class | Class "ExpressionSetIllumina" |
| exprs-method | Class "ExpressionSetIllumina" |
| exprs<- | 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 |
| illuminaChannel-class | Class "illuminaChannel" |
| illuminaOutlierMethod | Identifier outliers on an array section |
| imageplot | imageplot for beadLevelData object |
| insertBeadData | Add or modify 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 |
| 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" |
| openTIFF | Read the Illumina tiff images |
| 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 |
| 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. |
| se.exprs-method | Class "ExpressionSetIllumina" |
| se.exprs<- | 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 | Class "ExpressionSetIllumina" |
| show-method | Class "beadLevelData" |
| showArrayMask | Show Array Mask |
| summarize | Create a summarized object |
| [-method | Class "ExpressionSetIllumina" |
| [[-method | Class "beadLevelData" |