Man pages for beadarray
Quality assessment and low-level analysis for Illumina BeadArray data
| addFeatureData | Add probe data |
| annotationInterface | Storage of annotation information |
| 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 |
| beadarray-package | The beadarray package: a tool for low-level analysis of... |
| beadarrayUsersGuide | View beadarray User's Guide |
| boxplot | Boxplots from summary data |
| calculateDetection | Calculate detection scores |
| calculateOutlierStats | Outlier distribution stats |
| checkRegistration | Perform check for misregistered array segments. |
| class-beadLevelData | Class "beadLevelData" |
| class-BeadLevelList | Class "BeadLevelList" |
| class-beadRegistrationData | Class "beadRegistrationData" |
| class-ExpressionSetIllumina | Class "ExpressionSetIllumina" |
| class-illuminaChannel | Class "illuminaChannel" |
| class-limmaResults | Class "limmaResults" |
| combine | Combine two objects. |
| controlProbeDetection | Percentage of beads detected |
| convertBeadLevelList | Convert a BeadLevelList object into a beadLevelData object |
| createTargetsFile | A function to generate a targets file given a directory of... |
| deprecatedFunctions | Deprecated Functions |
| dim | Retrieve the dimensions of an object |
| expressionQCPipeline | Flexible bead-level QC pipeline |
| generateNeighbours | Generate matrix of neighbouring beads |
| GEO | Create files for a Gene Expression Omnibus submission |
| GEOtemplate | GEO required fields |
| getBeadData | Get raw data from a beadLevelData object |
| HULK | HULK - Bead Array Normalization by NEighbourhood Residuals |
| identifyControlBeads | Classify each bead according to its control status |
| illuminaOutlierMethod | Identifier outliers on an array section |
| imageplot | imageplot for beadLevelData object |
| imageProcessing | Image processing functions |
| insertBeadData | Add, modify or remove data in a beadLevelData object |
| insertSectionData | Modify the sectionData slot |
| limmaDE | Differential expression using limma |
| makeControlProfile | Retrieve control beads |
| makeQCTable | Tabulate QC scores |
| maplots | Function to construct the classic MA plots from a dataset |
| medianNormalise | Median normalise data in a matrix |
| metrics | Accessing metrics information in bead-level objects |
| noOutlierMethod | returns no outliers on an array section |
| normaliseIllumina | Normalise Illumina expression data |
| numBeads | Gets the number of beads from a beadLevelData object |
| outlierplot | Plot outlier locations |
| platformSigs | Annotation definitions |
| plotBeadIntensities | Plotting the intensities of selected beads on a section |
| plotBeadLocations | Plot bead locations |
| plotChipLayout | Function to Plot the Layout of an Illumina BeadChip |
| plotMAXY | Scatter plots and MA-plots for all specified arrays |
| plotTIFF | Produce plots of the Illumina tiff images |
| poscontPlot | Plot the positive controls |
| processSwathData | Prepare iScan data for use with beadarray |
| 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. |
| readTIFF | Read the Illumina tiff images |
| sampleSheet | Read a Sample sheet for a BeadArray experiment |
| sectionNames | Gets the section names from a beadLevelData Object |
| setWeights | Set weights from BASH |
| show | Display object summary |
| showArrayMask | Show Array Mask |
| squeezedVarOutlierMethod | Identifier outliers on an array section |
| summarize | Create a summarized object |
| transformationFunctions | Functions for transforming the data store in a... |
| weightsOutlierMethod | returns all beads with weight=0. |
