Question: What are the 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.
MAGE-TAB format files (see Sourceforge overview) can be divided into two groups: array data files and descriptive files.
There are two types of array data files:
- Raw array data – A variety of raw data files, produced by several different scanner makes and models, are supported by the caArray MAGE-TAB parser. However, these raw data may not be in MAGE-TAB format.
- Derived array data – Derived array data refers to either normalized array data, or a data file with data combined from more than one hybridization or scan. The caArray MAGE-TAB parser supports Affymetrix .CHP format for derived data (which is not in MAGE-TAB format). For the rest, derived data needs to be reformatted in a MAGE-TAB Data Matrix according to the table below.
MAGE-TAB Descriptive files can be divided into 3 subgroups:
- Array Design File (ADF),
- Investigation Design File (IDF)
- Sample Data Relationship File (SDRF). For more information about annotation files: IDF/SDRF, refer to caArray 008 - How do I use the Annotation Tab versus MAGE-TAB Annotation Files in caArray?.
The following table summarizes the definition of each MAGE-TAB format file.
Note that a MAGE-TAB format Array Design File (ADF) is not mandatory, since array design files for the common arrays are usually available from their respective array providers. If an array design file (which may not be MAGE-TAB format) is available from its array provider, you should choose it over an ADF. Third party array design files are uploaded using the Manage Array Design interface under caArray's Curation tab. An ADF file, on the other hand, can be uploaded together with the rest of MAGE-TAB files. An ADF file is not be validated or parsed by caArray. It will be imported directly into caArray according to the table that follows.
MAGE-TAB Formatted Files
Abbreviation |
File Type |
Description |
caArray compatible? |
Processed by caArray? |
|---|---|---|---|---|
IDF |
Investigation Design File |
Provides an overview of the experiment, including the experimental variables (factors) used, protocols, quality control strategy, publication information and contact details |
Yes |
Yes: Parsed, Validated before import |
SDRF |
Sample Data Relationship File |
Describes relationships between samples, arrays, data files, protocols, factor values etc. It is a table in which each hybridization channel is represented by a row, and columns represent the steps of the experiment. The ordering of these columns is important, and reads left-to-right in chronological order. |
Yes |
Yes: Parsed, Validated before import |
ADF |
Array Design File |
Provides the array-level annotation for the experiment. It relates the row-level identifiers in the data files to biological sequence annotation |
Yes |
No. Directly Import |
TXT or other |
Data Matrix |
Contains processed array data files in tab-delimited text format. Rows may represent genes/ exons/ genomic locations. Columns represent samples or experimental conditions. |
Yes |
No. Directly Import |
What are MAGE-TAB Files?
The term of "MAGE-TAB Files" (refer to caArray 002 - How do I upload MicroArray Gene Expression Data into caArray?, step 2 for an example), has been used to refer not only MAGE-TAB formatted files as summarized in the table, but also files that are supported by MAGE-TAB parser mentioned in the last section. To be more specific, MAGE-TAB files also include the third party's raw array data files, derived data files and array design files from array providers, as shown in the illustration.
In summary, MAGE-TAB files map to each other. Together they represent the complete experiment.
Diagram Identifying Content of MAGE-TAB Files
According to the figure above, MAGE-TAB files can be divided into two categories: array data files, which are in ASCII or binary format, and descriptive files, which contain information about array design and investigation data. These two categories can be further subdivided as follows:
Array data files can either be raw (i.e., unprocessed) data files whose format is specified by a third-party vendor, or they can be derived (i.e., normalized) data files. The latter are either generic data in MAGE-TAB format, or Affymetrix .CHP files that are not in MAGE-TAB format but can still be parsed by caArray.
Descriptive files can contain information about investigation data or array design. Investigation data files conform to one of two specifications: Investigation Description File (IDF) or Sample and Data Relationship File (SDRF). Array design files conform to one of two specifications: MAGE-TAB formatted design files with a .ADF file extension, or non-MAGE-TAB formatted design files from third-party vendors that can still be parsed by 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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