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A B C D E F G H I L M N O P Q R S V misc
| addArrayMask | Array Mask |
| arrayNames | Gets the strip/array names from a BeadLevelList Object |
| arrayNames,BeadLevelList-method | Class "BeadLevelList" |
| backgroundControlPlot | QA measures based on bead-level negative controls |
| backgroundCorrect | Background correct a BeadLevelList object |
| backgroundCorrect,BeadLevelList,character,double,logical-method | Class "BeadLevelList" |
| backgroundCorrect,BeadLevelList-method | Background correct a BeadLevelList object |
| backgroundCorrect,RGList-method | Background correct a BeadLevelList object |
| 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 |
| BeadChipSummary | Interactive bead-level plotting |
| BeadLevelList | Class "BeadLevelList" |
| BeadLevelList-class | Class "BeadLevelList" |
| beadResids | Calculates per strip/array bead-level residuals |
| BGFilter | Background Filter |
| BGFilterWeighted | Weighted Background Filter |
| BLData | BeadLevelList objec from an example experiment |
| boxplotBeads | Box plot of bead intensities |
| BSData | ExpressionSetIllumina object for the example experiment |
| calculateBeadLevelScores | Quality assessment for expression chips |
| calculateDetection | Calculate detection scores |
| chooseClusters | Choose Clusters |
| class:ExpressionSetIllumina | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays. |
| clearArrayMask | Array Mask |
| closeImage | Close Image |
| combine,ExpressionSetIllumina,ANY-method | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays. |
| combine,ExpressionSetIllumina,ExpressionSetIllumina-method | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays. |
| combineBeadLevelLists | Combines data from two BeadLevelList objects |
| combineBeadLevelLists,BeadLevelList-method | Class "BeadLevelList" |
| copyBeadLevelList | Copies a BeadLevelList Object |
| copyBeadLevelList,BeadLevelList-method | Class "BeadLevelList" |
| createBeadSummaryData | Produce bead averages |
| denseRegions | Find Dense Regions of Points (as used in diffuse defect analysis). |
| Detection | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays. |
| Detection,ExpressionSetIllumina-method | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays. |
| Detection<- | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays. |
| Detection<-,ExpressionSetIllumina,matrix-method | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays. |
| dim,BeadLevelList-method | Class "BeadLevelList" |
| ExpressionControlData | Control annotation for Illumina expression chips |
| ExpressionSetIllumina-class | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays. |
| exprs,ExpressionSetIllumina-method | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays. |
| exprs<-,ExpressionSetIllumina,matrix-method | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays. |
| findAllOutliers | Find outliers on a given strip/array |
| findBeadStatus | Find Outliers |
| generateE | Generate Error Image for BeadLevelList object |
| generateNeighbours | Generate Neighbours Matrix for BeadLevelList object |
| getAnnotation | Storage of annotation information for Illumina expression chips |
| getArrayData | Get raw data from a BeadLevelList object |
| getArrayData,BeadLevelList-method | Class "BeadLevelList" |
| getControlAnno | Storage of annotation information for Illumina expression chips |
| getProbeIntensities | Find Outliers |
| getProbeIntensities,BeadLevelList-method | Find Outliers |
| getVariance | Gets the bead-type variances from an ExpressionSetIllumina Object |
| getVariance,ExpressionSetIllumina-method | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays. |
| gradientPlot | Quality assessment for expression chips |
| HULK | HULK - Bead Array Normalization by NEighbourhood Residuals |
| HULKResids | HULK - Residuals |
| imageplot | imageplot for BeadLevelList object |
| initialize,BeadLevelList-method | Class "BeadLevelList" |
| initialize,ExpressionSetIllumina-method | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays. |
| lmhPlot | Plot the bead-level hybridisation controls |
| medianNormalise | Median normalise data in a matrix |
| NoBeads | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays. |
| NoBeads,ExpressionSetIllumina-method | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays. |
| NoBeads<- | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays. |
| NoBeads<-,ExpressionSetIllumina,matrix-method | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays. |
| normaliseIllumina | Normalise Illumina expression data |
| numBeads | Gets the number of beads from a BeadLevelList object |
| numBeads,BeadLevelList-method | Class "BeadLevelList" |
| outlierPlot | Locations of outliers on an Illumina chip |
| pData,BeadLevelList-method | Class "BeadLevelList" |
| phenoData,BeadLevelList-method | Class "BeadLevelList" |
| plotBeadDensities | plot densities of bead intensities |
| plotBeadIntensities | Plot bead intensities |
| plotBeadLocations | Plot bead locations |
| plotMA | Show MA plots |
| plotMAXY | Scatter plots and MA-plots for all specified arrays |
| plotOnSAM | Show variation between all 96 arrays |
| plotRG | Plot bead-level data: R vs G intensities |
| plotTIFF | Produce plots of the Illumina tiff images |
| plotXY | XY plots for two samples |
| poscontPlot | Plot bead-level housekeeping and biotin controls |
| probePairsPlot | QA plot using perfect match and mismatch controls |
| qcBeadLevel | Generate simple diagnostic plots for Illumina bead-level data |
| QCInfo | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays. |
| QCInfo,ExpressionSetIllumina-method | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays. |
| QCInfo<- | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays. |
| QCInfo<-,ExpressionSetIllumina,list-method | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays. |
| rankInvariantNormalise | Rank Invariant normalise data in a matrix |
| readBeadSummaryData | Read BeadStudio gene expression output |
| readBGX | Read Illumina .bgx file into R |
| readIllumina | Read bead-level data into R |
| readLocs | Read the .locs file produced with each array |
| readQC | Read Illumina control intensities |
| readTIFF | Read the Illumina tiff images |
| removeArrayMask | Array Mask |
| SAMSummary | Interactive bead-level plotting |
| se.exprs,ExpressionSetIllumina-method | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays. |
| se.exprs<-,ExpressionSetIllumina,matrix-method | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays. |
| setAnnotation | Storage of annotation information for Illumina expression chips |
| setWeights | Set BeadLevelList Weights |
| show,BeadLevelList-method | Class "BeadLevelList" |
| show,ExpressionSetIllumina-method | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays. |
| showArrayMask | Array Mask |
| viewBeads | View Beads |
| [,ExpressionSetIllumina-method | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays. |
| [[,BeadLevelList,ANY,missing-method | Class "BeadLevelList" |