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Highlights for Building caArray's MAGE-TAB Annotation Files

Topic: caArray Usage

Release: Up to caArray 2.2

Date entered: 02/17/2009

Question

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

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Introduction

caArray has been designed to handle MAGE-TAB data using certain conventions. The caArray User Guide devotes more than one whole chapter to a section in Chapter 7 – Submitting Data to Importing MAGE-TAB and an entire appendix to working with MAGE-TAB files with useful information in caArray. The appendix specifically includes much specific detail from recognized data field fields to validation rules (Chapter 6: Submitting Data to an Experiment (page 87) and Appendix A: essential for importing MAGE-TAB in caArray (page 101)files. Highlights are outlined below to offer you a quick start.

Recognized Fields and Validation Rules for MAGE-TAB Annotation Files

• You may can describe your experiment in great detail with the convenience of managing MAGE-TAB filefiles in spreadsheet format. For example, a biomaterial (Sourcesource, Samplersample, Extractextract, or labeled Extractextract) named in one column can be followed by any number of Characteristics characteristics columns containing annotation information data about that biomaterial.
  However, it It should be noted that caArray does have has requirements about which fields should be used and the order in which order they should 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.
  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)See Biomaterial Column Order in an SDRF.
• 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 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 Appendix A in the User's Guide.

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 have to 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) referred to referenced in SDRF files have to 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 have to must be uploaded, validated and imported in a separate session from IDF/DSRF files.
5. MAGE-TAB ADF and Data Matrix do not need to be validated. They can be imported directlyfiles 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 in caArray.

SDRF File Has Higher Priority

Annotation Annotations can be set configured via the "Annotation" user interface, Annotations tab in caArray or via an SDRF file , (refer to caArray008], Annotation (Annotations Tab vs. MAGE-TAB Annotation Files in caArray). The designation in the SDRF is authoritative. For example: the 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. See SDRF Decides Raw versus Derived Data File.

Known Bug List in caArray

Known Bug List for MAGE-TAB Files

Further Readings on MAGE-TAB Files

• For more information on MAGE-TAB Files, refer to caArray087 caArray 007 - MAGE-TAB Files.
• For more information on When when to Use use MAGE-TAB Annotation Files, refer to caArray008to caArray 008 - Using the Annotations tab or MAGE-TAB annotation files to annotate an experiment.
• For more information on How to upload MAGE-TAB files, refer to caArray002 caArray 002 - Uploading MicroArray Gene Expression Data into caArray.

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