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<strong>Applicable Releases:</strong> caArray 2.X
<strong>Date entered:</strong> 02/12/2009
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caArray Usage
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question}}Question: *What are the MAGE-TAB Files? * {{questionEnd
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Abbreviation |
File Type |
Comments |
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. |
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" (See an example)has been used to refer not only MAGE-TAB formatted files as summarized in table 1, but also files that are supported by MAGE-TAB parser mentioned in 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 figure below.
In summary, MAGE-TAB files refer to each other. Together they represent the complete experiment.
Building MAGE-TAB Formatted files
MAGE-TAB specification can be found at: MGED homepage.
To get start, you may generate a MAGE-TAB template file from EMBL-EBI's MAGE TAB site, or create your own IDF & SDRF files based on the MAGE-TAB documentation.
MAGE-TAB trainings and demos for the caArray users are currently under the development. We will add the links here once they become available.
Read more about When to use MAGE-TAB annotation files in caArray, Click Here
Read more on How to upload MAGE-TAB files, Click Here
Have a comment? Please leave your comment in caArray End User Forum
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