caArray Usage

Date entered: 02/17/2009

Release Up to: caArray 2.2

Question: *A Checklist: Building caArray's MAGE-TAB Annotation Files *

Answer:

caArray has been designed to handle MAGE-TAB data using certain conventions. caArray User Guide devotes more than one whole chapter on MAGE-TAB files with many useful information from recognized data field to validation rules (Chapter 6: Submitting Data to an Experiment Page 87 and Appendix A: MAGE-TAB in caArray Page 101). Highlights are outlined below to offer you a quick start.

Recognized Fields & Validation Rules for MAGE-TAB Annotation Files

1. You may describe your experiment in great details with the convenience of MAGE-TAB file. For example, a biomaterial (Source, Sampler, Extract, or labeled Extract) can be followed by any number of Characteristics columns containing annotation information about that biomaterials. However, it should be aware that caArray's does have requirement on which fields should be used and in which order they should be listed. For example, In SDRF file, 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, visit (caArray User Guide Appendix A, Page 107-Page 111).
2. Controlled vocabularies should be used in IDF and SDRF files. The common used vocabularies can be found in MGED Ontology (MO) or 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
3. All column types are not mandatory in the SDRF. caArray can Auto-generate missing biomaterials and associate protocols intelligently. |

MAGE-TAB Files: Upload & Import

1. MAGE-TAB Files have to be imported into experiments. That is, a 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) referred in SDRF files have to be validated and imported together.
4. Data files that are not referred by SDRF file can also be imported into the same experiment. But they have to be uploaded/validated/imported in a separate session from IDF/DSRF files
5. ADF and Data Matrix do not need to be validated. They can be imported directly. |

SDRF File Has Higher Priority

Annotation can be set via "Annotation" user interface, or via SDRF file, (see Annotation Tab vs. MAGE-TAB Annotation Files in caArray). The designation in the SDRF is authoritative. For example: the tissue site for one sample is set to be "Lung" from the annotation interface, but it is set to be "Brain" in the SDRF file. Upon data upload, the tissue site will be shown as "Brain", since SDRF file has higher priority over "Annotation" interface. |

Known Bug List in caArray

Further Readings on MAGE-TAB Files

• For more information on MAGE-TAB Files, Click Here
• For more information on When to Use MAGE-TAB Annotation Files, Click Here
• Read more on How to upload MAGE-TAB files, Click Here