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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). The MAGE-TAB specification document and related publications provide more details on the format.

MAGE-TAB File Types

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

File Type

File Extension

Description

Processed by caArray

Investigation Description Format (IDF)

.idf

A tab-delimited file providing general information about the investigation, including its name, a brief description, the investigator's contact details, bibliographic references, ontologies/databases referenced and free text descriptions of the protocols used in the investigation.

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.

Yes. Parsed, validated before import

Sample and Data Relationship Format (SDRF)

.sdrf

A tab-delimited file (or files) describing the relationships between samples, arrays, data, and other objects used or produced in the investigation, and providing all MIAME information that is not provided elsewhere. An SDRF contains all of the information linking the samples to your data files, (for example, Affymetrix CEL, Affymetrix CHP). Each row in the table represents a hybridization channel, and the columns represent the steps of the experiment, read from left to right.

Yes. Parsed, validated before import

Array Design Format (ADF)

.adf

A tab-delimited file with standardized column names describing defining the design of an array, e.g., what sequence is located at each position on an array and what the annotation of this sequence is. In caArray 2.4, MAGE-TAB ADF files can be uploaded but they are not parsed. MAGE-TAB ADF files are not required in a caArray experiment.

Can be uploaded, but are not parsed. Vendor-specific Array Design Files are recommended, if available.

Can be uploaded, but are not parsed. Vendor-specific Array Design Files are recommended, if available.

Data Matrix (ADF)

.txt or other

Contains processed array data files in tab-delimited text format.

Only copy number data matrix files parsed

In addition to the MAGE-TAB file types described above, the MAGE-TAB specification defines one additional file type to fully describe a microarray investigation: Raw and processed data files – ASCII or binary files, typically in their native formats; alternatively, data may also be provided in a specially defined tab-delimited format termed a "data matrix", described in the table above.

See also About File Types in caArray and MAGE-TAB in caArray--Overview.

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 process.

diagram illustrating the relationships of MAGE-TAB files to data files in caArray

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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