| findByCdf2 {aroma.affymetrix} | Non-documented objects |
| findByChipType.AffymetrixCdfFile {aroma.affymetrix} | Locates a CDF file from its chip type |
| findByChipType.AffymetrixCdfFile {aroma.affymetrix} | Locates a CDF file from its chip type |
| findByChipType.AffymetrixPgfFile {aroma.affymetrix} | Locates a PGF file from its chip type |
| findByChipType.AffymetrixPgfFile {aroma.affymetrix} | Locates a PGF file from its chip type |
| findByChipType.AromaChipTypeAnnotationFile {aroma.affymetrix} | Locates an annotation file by its chip type |
| findUnitsTodo.FirmaModel {aroma.affymetrix} | Identifies non-fitted units |
| findUnitsTodo.ProbeLevelModel {aroma.affymetrix} | Identifies non-fitted units |
| findUnitsTodo.UnitModel {aroma.affymetrix} | Identifies non-fitted units |
| FirmaFile {aroma.affymetrix} | The FirmaFile class |
| FirmaFile.getCellIndices {aroma.affymetrix} | Retrieves tree list of cell indices for a set of units |
| FirmaModel {aroma.affymetrix} | The FirmaModel class |
| FirmaModel.calculateResidualSet {aroma.affymetrix} | Gets the set of residuals corresponding to the PLM |
| FirmaModel.getFirmaSet {aroma.affymetrix} | Gets the set of FIRMA results for this model |
| FirmaModel.getFitUnitGroupFunction {aroma.affymetrix} | Static method to get the low-level function that fits the PLM |
| FirmaSet {aroma.affymetrix} | The FirmaSet class |
| fit.FirmaModel {aroma.affymetrix} | Estimates the model parameters |
| fit.Model {aroma.affymetrix} | Estimates the model parameters |
| fit.ProbeLevelModel {aroma.affymetrix} | Estimates the model parameters |
| fit.SingleArrayUnitModel {aroma.affymetrix} | Estimates the model parameters |
