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| averagePixels | Read BeadArray information into R |
| backgroundCorrect | Background Correct a BeadLevelList object |
| 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 | Class "BeadLevelList" |
| BeadLevelNormalise | Bead Level Normalisation |
| BLData | BeadLevelList for the example experiment |
| BSData | ExpressionSetIllumina object for the example experiment |
| calculateBackground | Read BeadArray information into R |
| calculateForegroundIntensities | Read BeadArray information into R |
| cbind.BeadLevelList | Combine BeadLevelList or BeadSummaryList Objects |
| 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. |
| createBeadSummaryData | Produce bead averages |
| createBeadSummaryData, BeadLevelList-method | Find Outliers |
| createBeadSummaryData,BeadLevelList-method | Produce bead averages |
| createBeadSummaryDataSlow | 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 | Retrieve the Dimensions of a BeadLevelList |
| dimnames.BeadLevelList | Retrieve the Dimension Names of an BeadLevelList or BeadSummaryList Object |
| 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,matrix-method | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays. |
| findAllOutliers | Find outliers on array |
| findAllOutliers, BeadLevelList-method | Find Outliers |
| findAllOutliersSlow | Find outliers on array |
| findBeadStatus | Find Outliers |
| FindIlluminaSpotl | Display part of a TIFF Image |
| 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 |
| imageplot, BeadLevelList-methods | Class "BeadLevelList" |
| 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. |
| 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 |
| plotQC | Read and plot Illumina quality control information |
| plotXY | XY plots for two samples |
| print.BeadLevelList | Class "BeadLevelList" |
| QC | Illumina quality control 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 |
| rbind.BeadLevelList | Combine BeadLevelList or BeadSummaryList Objects |
| read.pgmfile | Read BeadArray information into R |
| readBeadLevelData | Read BeadArray information into R |
| readBeadSummaryData | Read bead summary data information into R |
| readBeadSummaryTargets | Create targets object |
| readBeadTargets | Create targets object |
| readCols | Read bead summary data information into R |
| readQC | Read and plot 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 |
| singleQCPlot | Read and plot Illumina quality control information |
| [,ExpressionSetIllumina-method | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays. |
| [.BeadLevelList | Class "BeadLevelList" |