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Question: What are MAGE-TAB Files?
Topic: caArray Usage
Release: caArray 2.X
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Answer
MAGE-TAB (MicroArray Gene Expression Tabular) files, considered the MAGE-TAB data set, refer to simple tab-delimited, spreadsheet-based files, which can be used for annotating and communicating microarray data in a MIAME compliant fashion. MAGE-TAB specification is based on the Microarray and Gene Expression Object Model (MAGE-OM). The MAGE-TAB specification document and related publications provide more details on the format.
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To load an experiment into caArray using the MAGE-TAB format, you must create the first two file types shown in the table above, IDF and SDRF. See Building MAGE-TAB Formatted Files. You also must make sure that the corresponding Array Design (the third file type) for your experiment has been loaded into caArray. The fourth file type, raw and/or derived (processed) data files are created by the instruments reading the array results.
The files described in the table make up the MAGE-TAB data set. They can be categorized into two groups: descriptive files and array data files. Some of the files are in MAGE-TAB format (see the Sourceforge overview) and others are supported as part of the MAGE-TAB data set. See the following figure and its description below.
The descriptive files include IDF, SDRF and Array Design Files. Note that the MAGE-TAB format Array Design File (designated as ADF) is not mandatory in caArray, since array design files for the common arrays are usually available from their respective array providers. If an array design file (which may not be MAGE-TAB format) is available from its array provider, it should be chosen over an ADF file. MAGE-TAB ADF files are not parsed by caArray. Array design files, whether native or ADF, are uploaded using the Manage Array Design interface under Curation on the caArray left sidebar. The MAGE-TAB file types, IDF, SDRF and data matrix files, on the other hand, are uploaded on the Manage Data page.
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See also About File Types in caArray and MAGE-TAB in caArray--Overview in the caArray User's Guide.
MAGE-TAB and Data Files Relationships
MAGE-TAB files imported into caARRAY map to data files also imported into the same caARRAY experiment. The following figure illustrates the processrelationship.
Building MAGE-TAB Formatted files
Because of the varied nature of every caArray experiment and its corresponding data, it is impossible to outline the exact steps for creating a caArray-compatible MAGE-TAB file. There are strict guidelines, however, for characteristics of MAGE-TAB files that meet the criteria. Refer to Appendix A - MAGE-TAB in caArray in the caArray User's Guide for specific details regarding caArray-compatible MAGE-TAB files. To provide context, see the MAGE-TAB Specification document.
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For more information about when to use MAGE-TAB annotation files in caArray, refer to caArray 008 - Should I use the Annotations Tab or MAGE-TAB annotation Files in caArray?. For more information on how to upload MAGE-TAB files, refer to Importing MAGE_TAB Files in the caArray User's Guide.
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