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There are two types of array data files: the raw
- Raw array data
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- – 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.
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- Derived array data – Derived array data refers to either
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- 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
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- 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 further divided into 3 subgroups:
- Array Design File (ADF),
- Investigation Design File (IDF)
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- 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 It is necessary to mention that 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 should be chosen over an ADF. Furthermore, MAGE-TAB ADF is not parsed by caArray. The third Third party array design files are uploaded via "using the Manage Array Design " interface under caArray's "Curation" tab. An ADF file, on the other hand, is can be uploaded together with the rest of MAGE-TAB files. An ADF file will 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 | Comments 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 |
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In summary, MAGE-TAB files refer map to each other. Together they represent the complete experiment.
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The MAGE-TAB specification can be found at: MGED homepage.
To get started, you may 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 refer to Appendix A - MAGE-TAB in caArray in the caArray User's Guide for detailed information about ensuring that your MAGE-TAB files are compatible with caArray's specificationstraining and demos for the caArray users are currently under the development. We will add the links here once they become available.
For more information about when 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 how to upload MAGE-TAB files, refer to Importing MAGE_TAB Files in the caArray User's Guide.
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