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h1. 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:
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h2. 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|http://www.mged.org/Workgroups/MIAME/miame.html]. MAGE-TAB specification is based on the [Microarray and Gene Expression|http://www.mged.org/Workgroups/MAGE/mage.html] Object Model ([MAGE-OM|http://www.mged.org/Workgroups/MIAME/miame_mage-om.html]). MAGE-TAB [specification|http://www.mged.org/mage-tab/spec1.0.html] and related [publications|http://www.biomedcentral.com/1471-2105/7/489] 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|https://wiki.nci.nih.gov/x/Oxo9Ag#7-SubmittingDatatoanExperiment-MAGETABincaArrayOverview]

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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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*Diagram Identifying Content of MAGE-TAB Files*
!MAGE-TAB-Files.jpg|align=center,alt="Diagram Identifying Content of MAGE-TAB Files"!


h3. 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|https://wiki.nci.nih.gov/x/Rho9Ag] in the caArray User's Guide for specific details regarding caArray-compatible MAGE-TAB files. To provide context, see the [MAGE-TAB Specification document|http://www.mged.org/mage-tab/spec1.0.html].

To get started, you can generate a MAGE-TAB template file from [EMBL-EBI's MAGE TAB site|http://www.mged.org/mage-tab/tools.html], or create your own IDF and SDRF files based on the [Sourceforge MAGE-TAB documentation|http://tab2mage.sourceforge.net/docs/magetab_docs.html].

Be sure and review the details in [Appendix A - MAGE-TAB in caArray|https://wiki.nci.nih.gov/x/Rho9Ag] 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?|caArray 008 - Should I use the Annotations tab or MAGE-TAB annotation files to annotate my experiment?].  For more information on how to upload MAGE-TAB files, refer to [Importing MAGE_TAB Files|https://wiki.nci.nih.gov/x/Oxo9Ag#7-SubmittingDatatoanExperiment-ImportingMAGETABData] in the caArray User's Guide.

h2. Have a comment?

Please leave your comment in the [caArray End User Forum|https://cabig-kc.nci.nih.gov/Molecular/forums/viewtopic.php?f=6&t=577].

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