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Topic: caArray Usage
Release: Up to caArray 2.2
Date entered: 02/17/2009
A Checklist: Building caArray's MAGE-TAB Annotation Files
caArray has been designed to handle MAGE-TAB data using certain conventions. The caArray User Guide devotes more than one whole chapter to MAGE-TAB files with 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.
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).
Annotation can be set via the "Annotation" user interface, or via an SDRF file, (refer to caArray008], 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 than "Annotation" interface.
Known Bug List for MAGE-TAB Files
Error Message |
Known Bugs |
---|---|
"Term Source Ref is not preceded by valid data type" |
Factor Value can not have "Term Source REF" followed |
Please leave your comment in the caArray End User Forum.