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caArray has been designed to handle MAGE-TAB data using certain conventions. The caArray User Guide devotes a section in Chapter 7 – Submitting Data to Importing MAGE-TAB and an entire appendix to working with MAGE-TAB files in caArray. The appendix specifically includes much specific detail from recognized data fields to validation rules essential for importing MAGE-TAB files. Highlights are outlined below to offer you a quick start.

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• You can describe your experiment in great detail with the convenience of managing MAGE-TAB files in spreadsheet format. For example, a biomaterial (source, sample, extract, or labeled extract) named in one column can be followed by any number of Characteristics characteristics columns containing annotation data about that biomaterial.
  It should be noted that caArray has requirements about which fields should be used and the order in which they must be listed. For example, in an SDRF file, the Biomaterials biomaterials columns must follow the order of Source Name - Sample Name - Extract Name - Labeled Extract Name. See Biomaterial Column Order in an SDRF.

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• SDRF

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• 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. See Term Source REF.
• All column types are not mandatory in the SDRF. caArray can auto-generate missing biomaterials and associate protocols intelligently.

For a detailed list of recognized fields and validation rules for IDF and SDRF files, refer to Aappendix A).

MAGE-TAB Files: Upload and Import

See Importing MAGE-TAB Data in the caArray User's Guide for more information about all points noted in this section.

1. MAGE-TAB Files must be [ imported into experiments. That is, an experiment needs to be created before MAGE-TAB files are imported.
2. Although only one IDF is allowed per import session, multiple IDF files are allowed per experiment.
3. IDF, SDRF(s), data file(s) referenced in SDRF files must be validated and imported together.
4. Data files that are not referred to by SDRF files can also be imported into the same experiment, but they must be uploaded, validated and imported in a separate session from IDF/DSRF files.
5. MAGE-TAB ADF and Data Matrix files can be uploaded, but caArray does not parse these files. the exception is copy number data matrix files, which caArray does parse. See [About File Types|https://wiki.nci.nih.gov/x/Oxo9Ag #7Oxo9Ag#7-SubmittingDatatoanExperiment-AboutFileTypesincaArray
   Create the MAGE-TAB files].

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