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| arrayNames | Gets the array names from a BeadLevelList Object |
| arrayNames,BeadLevelList-method | Class "BeadLevelList" |
| averagePixels | Read BeadArray information into R |
| backgroundCorrect | Background Correct a BeadLevelList object |
| backgroundCorrect,BeadLevelList,character,double,logical-method | Class "BeadLevelList" |
| backgroundCorrect,BeadLevelList-method | Background Correct a BeadLevelList object |
| backgroundCorrect,BeadLevelList-methods | Background Correct a BeadLevelList object |
| backgroundNormalise | Background Normalisation for Bead Summary Data objects |
| backgroundNormalise, ExpressionSetIllumina,ExpressionSetIllumina-method | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays. |
| backgroundNormalise, ExpressionSetIllumina-method | Background Normalisation for Bead Summary Data objects |
| backgroundNormalise, ExpressionSetIllumina-methods | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays. |
| BeadChipSummary | Interactive bead level plotting |
| BeadLevelList | Class "BeadLevelList" |
| BeadLevelList-class | Class "BeadLevelList" |
| BeadLevelNormalise | Bead Level Normalisation |
| BLData | BeadLevelList for the example experiment |
| boxplotBeads | Box plot of bead intensities |
| BSData | ExpressionSetIllumina object for the example experiment |
| calculateBackground | Read BeadArray information into R |
| calculateForegroundIntensities | Read BeadArray information into R |
| class:ExpressionSetIllumina | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays. |
| 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 a BeadLevelList Object |
| combineBeadLevelLists,BeadLevelList-method | Class "BeadLevelList" |
| copyBeadLevelList | Copies a BeadLevelList Object |
| copyBeadLevelList,BeadLevelList-method | Class "BeadLevelList" |
| createBeadSummaryData | Produce bead averages |
| createBeadSummaryData, BeadLevelList-method | Find Outliers |
| createBeadSummaryData,BeadLevelList-method | Produce bead averages |
| Detection | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays. |
| Detection,ExpressionSetIllumina-method | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays. |
| DiffScore | Illumina's DE statistic |
| dim,BeadLevelList-method | Class "BeadLevelList" |
| displayTIFFImage | Display part of a TIFF Image |
| 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,ANY-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 array |
| findAllOutliers, BeadLevelList-method | Find Outliers |
| findAllOutliers-methods | Find outliers on array |
| findBeadStatus | Find Outliers |
| FindIlluminaSpotl | Display part of a TIFF Image |
| getArrayData | Gets the raw intensity data from a BeadLevelList object |
| getArrayData,BeadLevelList-method | Class "BeadLevelList" |
| getProbeIndices | Find Outliers |
| getProbeIndicesC | Find Outliers |
| getProbeIntensities | Find Outliers |
| getProbeIntensities,BeadLevelList-method | Find Outliers |
| IdentifyBeads | Display part of a TIFF Image |
| IdentifyIntensity | Display part of a TIFF Image |
| imageplot | imageplot for BeadArrays object |
| initialize,BeadLevelList-method | Class "BeadLevelList" |
| initialize,ExpressionSetIllumina-method | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays. |
| LargeDataObject-class | Large Data Object - class |
| medianNormalise | Median Normalisation for BeadLevelList objects |
| NoBeads | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays. |
| NoBeads,ExpressionSetIllumina-method | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays. |
| numBeads | Gets the number of beads from a BeadLevelList object |
| numBeads,BeadLevelList-method | Class "BeadLevelList" |
| pData,BeadLevelList-method | Class "BeadLevelList" |
| phenoData,BeadLevelList-method | Class "BeadLevelList" |
| plotBeadDensities | plot density of bead intensities |
| plotBeadIntensities | Plot bead intensities |
| plotBeadLocations | Show 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 |
| plotXY | XY plots for two samples |
| QC | Illumina quality control data |
| 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. |
| rankInvariantNormalise | Rank Invariant Normalisation for Bead Summary data |
| read.pgmfile | Read BeadArray information into R |
| readBeadLevelData | Read BeadArray information into R |
| readBeadSummaryData | Read BeadStudio gene expression output |
| readBeadSummaryTargets | Create targets object |
| readBeadTargets | Create targets object |
| readIllumina | Read BeadArray information into R |
| readQC | Read Illumina quality control information |
| 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. |
| sharpen | Read BeadArray information into R |
| show,BeadLevelList-method | Class "BeadLevelList" |
| show,ExpressionSetIllumina-method | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays. |
| show,LargeDataObject-method | Large Data Object - class |
| showTIFF | Display part of a TIFF Image |
| [,ExpressionSetIllumina-method | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays. |
| [[,BeadLevelList,ANY,missing-method | Class "BeadLevelList" |