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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.

MAGE-TAB format uses four different types of files to capture information about an experiment. See also [#About File Types in caArray]. 
|| File Type || File Extension || Description || Processed by caArray||
| Investigation Description Format (*IDF*) | .idf | Provides general information about the experiment, including its name, a brief description, the investigator‘s contact details, bibliographic references, and ontologies/databases referenced.  {warning:title=Warning}  In a tab-separated line in the IDF, there must be no empty columns, i.e. two tabs with nothing between them. Empty columns will result in import failure.{warning}|Yes. Parsed, validated before import|
| Sample and Data Relationship Format (*SDRF*) | .sdrf | An SDRF file describes relationships between samples, arrays, data files, protocols, factor values, etc. Each row in the table represents a hybridization channel, and the columns represent the steps of the experiment, read from left to right. An SDRF contains all of the information linking the samples to your data files, (for example, Affymetrix CEL, Affymetrix CHP). See example in the following figure.|Yes. Parsed, validated before import|
| Array Design Format (*ADF*) | .adf | Defines each array type used. In caArray 2.4, ADF files can be uploaded but they are not parsed. Not required in a caArray experiment. |Can be uploaded, but are not parsed. Vendor-specific ADF files required instead.|
| Data Matrix (*ADF*) | .txt or other | Contains processed array data files in tab-delimited text format. | Only copy number data matrix files parsed|

For more information see [MAGE-TAB in caArray--Overview|https://wiki.nci.nih.gov/x/Oxo9Ag#7-SubmittingDatatoanExperiment-MAGETABincaArrayOverview]

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

!MAGE-TAB relationships2.png|vspace=4, border=1, alt="diagram illustrating the relationships of MAGE-TAB files to data files in caArray"!


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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