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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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<b>Table 1. MAGE-TAB Formatted Files</b>

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.
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" (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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