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| oligo-package | The oligo package: a tool for low-level analysis of oligonucleotide arrays |
| basecontent | Sequence Base Contents |
| basicRMA | Simplified Interface to RMA |
| bg | Accessors and replacement methods for the PM/MM/BG matrices. |
| bg,FeatureSet-method | Accessors and replacement methods for the PM/MM/BG matrices. |
| bg,TilingFeatureSet2-method | Accessors and replacement methods for the PM/MM/BG matrices. |
| bg<- | Accessors and replacement methods for the PM/MM/BG matrices. |
| bg<-,FeatureSet,matrix-method | Accessors and replacement methods for the PM/MM/BG matrices. |
| bg<-,TilingFeatureSet2,array-method | Accessors and replacement methods for the PM/MM/BG matrices. |
| boxplot | Boxplot |
| boxplot,ExpressionSet-method | Boxplot |
| boxplot,FeatureSet-method | Boxplot |
| cleanPlatformName | Parser to CEL files |
| crlmm | Genotype Calls |
| getContainer | Get container information for NimbleGen Tiling Arrays. |
| getContainer,TilingFeatureSet-method | Get container information for NimbleGen Tiling Arrays. |
| getContainer-methods | Get container information for NimbleGen Tiling Arrays. |
| getCrlmmSummaries | Function to get CRLMM summaries saved to disk |
| getNgsColorsInfo | Helper function to extract color information for filenames on NimbleGen arrays. |
| getX | Accessors for physical array coordinates. |
| getX,DBPDInfo-method | Accessors for physical array coordinates. |
| getX,FeatureSet-method | Accessors for physical array coordinates. |
| getX-methods | Accessors for physical array coordinates. |
| getY | Accessors for physical array coordinates. |
| getY,DBPDInfo-method | Accessors for physical array coordinates. |
| getY,FeatureSet-method | Accessors for physical array coordinates. |
| getY-methods | Accessors for physical array coordinates. |
| hist | Density estimate |
| hist,ExpressionSet-method | Density estimate |
| hist,FeatureSet-method | Density estimate |
| image | Display a Color Image |
| image,FeatureSet-method | Display a Color Image |
| justCRLMM | Genotype Calls |
| justSNPRMA | Summarization of SNP data |
| list.celfiles | List CEL/XYS files |
| list.xysfiles | List CEL/XYS files |
| MAplot | MA plots |
| MAplot,FeatureSet-method | MA plots |
| MAplot-methods | MA plots |
| mm | Accessors and replacement methods for the PM/MM/BG matrices. |
| mm,FeatureSet-method | Accessors and replacement methods for the PM/MM/BG matrices. |
| mm,TilingFeatureSet2-method | Accessors and replacement methods for the PM/MM/BG matrices. |
| mm<- | Accessors and replacement methods for the PM/MM/BG matrices. |
| mm<-,FeatureSet,matrix-method | Accessors and replacement methods for the PM/MM/BG matrices. |
| mm<-,TilingFeatureSet2,array-method | Accessors and replacement methods for the PM/MM/BG matrices. |
| plotM | Methods for Log-Ratio plotting |
| plotM,SnpQSet,character-method | Methods for Log-Ratio plotting |
| plotM,SnpQSet,integer-method | Methods for Log-Ratio plotting |
| plotM,SnpQSet,numeric-method | Methods for Log-Ratio plotting |
| plotM,TilingQSet,missing-method | Methods for Log-Ratio plotting |
| plotM-methods | Methods for Log-Ratio plotting |
| pm | Accessors and replacement methods for the PM/MM/BG matrices. |
| pm,FeatureSet-method | Accessors and replacement methods for the PM/MM/BG matrices. |
| pm,TilingFeatureSet2-method | Accessors and replacement methods for the PM/MM/BG matrices. |
| pm<- | Accessors and replacement methods for the PM/MM/BG matrices. |
| pm<-,FeatureSet,matrix-method | Accessors and replacement methods for the PM/MM/BG matrices. |
| pm<-,TilingFeatureSet2,array-method | Accessors and replacement methods for the PM/MM/BG matrices. |
| read.celfiles | Parser to CEL files |
| read.celfiles2 | Parser to CEL files |
| read.xysfiles | Parser to XYS files |
| read.xysfiles2 | Parser to XYS files |
| readSummaries | Read summaries generated by crlmm |
| rma | RMA - Robust Multichip Average algorithm |
| rma,ExonFeatureSet-method | RMA - Robust Multichip Average algorithm |
| rma,ExpressionFeatureSet-method | RMA - Robust Multichip Average algorithm |
| rma,GeneFeatureSet-method | RMA - Robust Multichip Average algorithm |
| sequenceDesignMatrix | Create design matrix for sequences |
| snprma | Preprocessing SNP Arrays |