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Topic: caArray Usage
Release: Up to caArray 2.2
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- You may describe your experiment in great detail with the convenience of MAGE-TAB file. For example, biomaterial (Source, Sampler, Extract, or labeled Extract) can be followed by any number of Characteristics columns containing annotation information about that biomaterial.
However, it should be noted that caArray does have requirements about which fields should be used and in which order they should be listed. For example, in an SDRF file, the Biomaterials columns must follow the order of Source Name - Sample Name - Extract Name - Labeled Extract Name.
For a detailed list of recognized fields and validation rules for IDF and SDRF files, refer to the caArray User Guide (Appendix A, page 107-page 111). - Controlled vocabularies should be used in IDF and SDRF files. The commonly used vocabularies can be found in MGED Ontology (MO) or the NCI Thesaurus. Each TERM SOURCE REF should have an entry in the IDF file. If term source is unknown, use "caArray" in the TERM SOURCE REF column.
- All column types are not mandatory in the SDRF. caArray can Auto-generate missing biomaterials and associate protocols intelligently.
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