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 and Associated File Types
The MAGE-TAB specification defines four different types of files to fully describe a microarray investigation. The following table summarizes the definition for each of these file types.
File Type |
File Extension |
Description |
Processed by caArray |
|---|---|---|---|
Investigation Description Format (IDF) |
.idf |
A MAGE-TAB 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 MAGE-TAB 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 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. 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. |
Raw and processed data files |
.txt or other |
Raw data files: ASCII or binary files, typically in their native formats. Processed (derived) data: tab-delimited text format; can be MAGE-TAB data matrix files. |
Of data matrix files, only copy number data matrix files are parsed. |
To load an experiment into caArray using the MAGE-TAB format, you must create the first two file types, IDF and SDRF. See Building MAGE-TAB Formatted Files for details on making IDF and SDRF 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.
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 process.
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.
It is essential that you 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 - 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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