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caArray Usage
Date entered: 02/17/2009
Release Up to: caArray 2.2
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Highlights for Building caArray's MAGE-TAB Annotation Files
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Topic: caArray Usage
Release: Up to caArray 2.2
Date entered: 02/17/2009
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Introduction
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Question
Answer
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Answer:
caArray has been designed to handle MAGE-TAB data using certain conventions. The caArray User Guide devotes more than one whole chapter on a section in Chapter 7 – Submitting Data to Importing MAGE-TAB and an entire appendix to working with MAGE-TAB files with many 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
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and Validation Rules for MAGE-TAB Annotation Files
- You
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- can describe your experiment in great
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- detail with the convenience of managing MAGE-TAB
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- files in spreadsheet format. For example, a biomaterial (
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- source,
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- sample,
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- extract, or labeled
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- extract) named in one column can be followed by any number of
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- characteristics columns containing annotation
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- data about that
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- biomaterial.
It should be
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- noted that caArray
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- has requirements about which fields should be used and the order in which
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- they
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- must be listed. For example,
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- in an SDRF file,
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- the biomaterials columns must follow the order of Source Name - Sample Name - Extract Name - Labeled Extract Name.
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- See Biomaterial Column Order in an SDRF.
- Controlled vocabularies should be used in IDF and SDRF files. The
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- 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
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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
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and Import
See Importing MAGE-TAB Data in the caArray User's Guide for more information about all points noted in this section.
- MAGE-TAB Files must Files have to be imported into experiments. That is, a an experiment needs to be created before MAGE-TAB files are imported.
- Although only one IDF is allowed per import session, multiple IDF files are allowed per experiment.
- IDF, SDRF(s), data file(s) referred referenced in SDRF files have to must be validated and imported together.
- Data files that are not referred to by SDRF file files can also be imported into the same experiment. But they have to , but they must be uploaded/, validated /and imported in a separate session from IDF/DSRF files.
- MAGE-TAB ADF and Data Matrix do not need to be validated. They can be imported directly. |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 in caArray.
SDRF File Has Higher Priority
Annotation Annotations can be set via "Annotation" user interface, configured via the Annotations tab in caArray or via an SDRF file , (see 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 over than "Annotation" interface. |See SDRF Decides Raw versus Derived Data File.
Known Bug List in caArray
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Known Bug List for MAGE-TAB Files
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Error Message | Known Bugs |
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"Term Source Ref is not preceded by valid data type" | Factor Value can not have "Term Source REF" followed |
Further Readings on MAGE-TAB Files
- For more information on MAGE-TAB Files, Click Hererefer to caArray 007 - MAGE-TAB Files.
- For more information on When when to Use use MAGE-TAB Annotation Files, Click Hererefer to caArray 008 - Using the Annotations tab or MAGE-TAB annotation files to annotate an experiment.
- For more information Read more on How to upload MAGE-TAB files, Click Here
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Please leave your comment in the caArray End User Forum
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