| Function | Description |
| addDerivedData | Adding a derived dataset to an existing MAGEML document |
| addNormToMAGEML | Adding a norm object to an existing MAGEML document |
| getArrayID | Get ArrayID's |
| getArrayLayout | Creation of a marrayLayout object |
| getArrayLayoutLimma | Get layout for limma |
| getGnames | Creation of a Gnames marrayInfo object |
| getNumberOfFeatures | Retrieves number of features |
| getOrganization | Retrieves Organization who did experiment |
| getQTDimensions | Retrieves QuantitationType Dimensions |
| getQTypeDescription | Retrieves description of a QuantitationType |
| getQuantitationTypes | Retrieves QuantitationTypes from an experiment |
| importMAGEML | import MAGEML documents |
| importMAGEOM | import MAGEOM of MAGEML documents |
| JavaVMRef-class | JavaVMRef |
| makeEset | Creation of a exprSet object |
| makeMarrayRaw | Creation of a marrayRaw object |
| makeRG | Creation of a RGList object |
| MEXP14 | Example dataset in MAGEML-format |
| reset | reset |
| writeMAGEML | write MAGEML documents |