A B C D E G H I L M N O P Q R S W misc
| beadarray-package | The beadarray package: a tool for low-level analysis of Illumina BeadArrays |
| addFeatureData | Add probe data |
| annotation | Storage of annotation information |
| annotation-method | Storage of annotation information |
| annotation<--method | Storage of annotation information |
| arrayNames | Deprecated Functions |
| arrayNames-method | Class "BeadLevelList" |
| ArrayWeights | Class "limmaResults" |
| ArrayWeights-method | Class "limmaResults" |
| ArrayWeights<- | Class "limmaResults" |
| ArrayWeights<--method | Class "limmaResults" |
| 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 | Class "beadLevelData" |
| BeadLevelList-class | Class "BeadLevelList" |
| beadRegistrationData-class | Class "beadRegistrationData" |
| beadStatusVector | Classify each bead according to its control status |
| boxplot-method | Boxplots from summary data |
| boxplot-method | Class "beadLevelData" |
| boxplot-method | Class "beadRegistrationData" |
| calculateDetection | Calculate detection scores |
| calculateOutlierStats | Outlier distribution stats |
| checkPlatform | Deprecated Functions |
| checkRegistration | Perform check for misregistered array segments. |
| combine-method | Combine two objects. |
| combinedControlPlot | Flexible bead-level QC pipeline |
| ContrastMatrix | Class "limmaResults" |
| ContrastMatrix-method | Class "limmaResults" |
| ContrastMatrix<- | Class "limmaResults" |
| ContrastMatrix<--method | Class "limmaResults" |
| controlProbeDetection | Percentage of beads detected |
| convertBeadLevelList | Convert a BeadLevelList object into a beadLevelData object |
| createBeadSummaryData | Deprecated Functions |
| createGEOMatrix | Create files for a Gene Expression Omnibus submission |
| createGEOMeta | Create files for a Gene Expression Omnibus submission |
| createTargetsFile | A function to generate a targets file given a directory of Illumina bead-level files |
| DesignMatrix | Class "limmaResults" |
| DesignMatrix-method | Class "limmaResults" |
| DesignMatrix<- | Class "limmaResults" |
| DesignMatrix<--method | Class "limmaResults" |
| Detection | Class "ExpressionSetIllumina" |
| Detection-method | Class "ExpressionSetIllumina" |
| Detection<- | Class "ExpressionSetIllumina" |
| Detection<--method | Class "ExpressionSetIllumina" |
| dim-method | Class "limmaResults" |
| dim-method | Retrieve the dimensions of an object |
| expressionQCPipeline | Flexible bead-level QC pipeline |
| ExpressionSetIllumina-class | Class "ExpressionSetIllumina" |
| exprs-method | Class "ExpressionSetIllumina" |
| exprs<--method | Class "ExpressionSetIllumina" |
| generateNeighbours | Generate matrix of neighbouring beads |
| genericBeadIntensityPlot | Plotting the intensities of selected beads on a section |
| getAnnotation | Deprecated Functions |
| getArrayData | Deprecated Functions |
| getArrayData-method | Class "BeadLevelList" |
| getBeadData | Get raw data from a beadLevelData object |
| getControlProfile | Storage of annotation information |
| greenChannel | Class "illuminaChannel" |
| greenChannelTransform | Functions for transforming the data store in a 'beadLevelData' object for easier visualisation or summarisation. |
| HULK | HULK - Bead Array Normalization by NEighbourhood Residuals |
| identifyControlBeads | Classify each bead according to its control status |
| illuminaBackground | Image processing functions |
| illuminaChannel-class | Class "illuminaChannel" |
| illuminaForeground | Image processing functions |
| illuminaOutlierMethod | Identifier outliers on an array section |
| illuminaSharpen | Image processing functions |
| imageplot | imageplot for beadLevelData object |
| insertBeadData | Add, modify or remove data in a beadLevelData object |
| insertSectionData | Modify the sectionData slot |
| limmaDE | Differential expression using limma |
| limmaResults-class | Class "limmaResults" |
| LogFC | Class "limmaResults" |
| LogFC-method | Class "limmaResults" |
| LogFC<- | Class "limmaResults" |
| LogFC<--method | Class "limmaResults" |
| logGreenChannelTransform | Functions for transforming the data store in a 'beadLevelData' object for easier visualisation or summarisation. |
| LogOdds | Class "limmaResults" |
| LogOdds-method | Class "limmaResults" |
| LogOdds<- | Class "limmaResults" |
| LogOdds<--method | Class "limmaResults" |
| 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. |
| makeControlProfile | Retrieve control beads |
| makeGEOSubmissionFiles | Create files for a Gene Expression Omnibus submission |
| makeQCTable | Tabulate QC scores |
| medianBackground | Image processing functions |
| medianNormalise | Median normalise data in a matrix |
| metaTemplate | GEO required fields |
| metrics | Accessing metrics information in bead-level objects |
| metrics-method | Accessing metrics information in bead-level objects |
| nObservations | Class "ExpressionSetIllumina" |
| nObservations-method | Class "ExpressionSetIllumina" |
| nObservations<- | Class "ExpressionSetIllumina" |
| nObservations<--method | Class "ExpressionSetIllumina" |
| noOutlierMethod | returns no outliers on an array section |
| normaliseIllumina | Normalise Illumina expression data |
| numBeads | Gets the number of beads from a beadLevelData object |
| numBeads-method | Class "beadLevelData" |
| outlierplot | Plot outlier locations |
| p95 | Accessing metrics information in bead-level objects |
| p95-method | Accessing metrics information in bead-level objects |
| platformSigs | Annotation definitions |
| plot-method | Class "limmaResults" |
| 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 |
| plotMA-method | Function to construct the classic MA plots from a dataset |
| 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 |
| processSwathData | Prepare iScan data for use with beadarray |
| PValue | Class "limmaResults" |
| PValue-method | Class "limmaResults" |
| PValue<- | Class "limmaResults" |
| PValue<--method | Class "limmaResults" |
| qcData | Class "ExpressionSetIllumina" |
| qcData-method | Class "ExpressionSetIllumina" |
| quickSummary | Create summary values for specified IDs |
| readBeadSummaryData | Read BeadStudio gene expression output |
| readIdatFiles | Read BeadScan gene expression output |
| readIllumina | Read bead-level Illumina data |
| readLocsFile | Read ".locs" file. |
| readSampleSheet | Read a Sample sheet for a BeadArray experiment |
| readTIFF | Read the Illumina tiff images |
| redChannelTransform | Functions for transforming the data store in a 'beadLevelData' object for easier visualisation or summarisation. |
| removeBeadData | Add, modify or remove data in a beadLevelData object |
| sampleSheet | Read a Sample sheet for a BeadArray experiment |
| sampleSheet-method | Read a Sample sheet for a BeadArray experiment |
| sampleSheet<- | Read a Sample sheet for a BeadArray experiment |
| sampleSheet<--method | Read a Sample sheet for a BeadArray experiment |
| se.exprs-method | Class "ExpressionSetIllumina" |
| se.exprs<--method | Class "ExpressionSetIllumina" |
| sectionNames | Gets the section names from a beadLevelData Object |
| sectionNames-method | Class "beadLevelData" |
| setAnnotation | Deprecated Functions |
| setWeights | Set weights from BASH |
| show-method | Display object summary |
| showArrayMask | Show Array Mask |
| snr | Accessing metrics information in bead-level objects |
| snr-method | Accessing metrics information in bead-level objects |
| squeezedVarOutlierMethod | Identifier outliers on an array section |
| suggestAnnotation | Storage of annotation information |
| summarize | Create a summarized object |
| weightsOutlierMethod | returns all beads with weight=0. |
| [-method | Class "ExpressionSetIllumina" |
| [-method | Class "limmaResults" |
| [[-method | Class "beadLevelData" |