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Question: What are MAGE-TAB Files?

Topic: caArray Usage

Release: caArray 2.X

Date entered: 02/12/2009

Topics on this page include the following:

Answer

MAGE-TAB (MicroArray Gene Expression Tabular) format files 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). MAGE-TAB specification and related publications provide more details on the format.

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The following table summarizes the definition of each MAGE-TAB format file.

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For more information see MAGE-TAB in caArray--Overview

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MAGE-TAB files imported into caARRAY map to data files also imported into the same caARRAY experiment. The following figure illustrates the process.

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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.

To get started, you can generate a MAGE-TAB template file from EMBL-EBI's MAGE TAB site, or create your own IDF and SDRF files based on the Sourceforge MAGE-TAB documentation.

Be sure and review the details in Appendix A - MAGE-TAB in caArray to ensure that your MAGE-TAB files meet the specifications for compatibility with caArray.

For more information about when to use MAGE-TAB annotation files in caArray, refer to [caArray 008 - How do I use the Annotation Tab versus 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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