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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 of each MAGE-TAB format filefor each of these file types.

File Type

File Extension

Description

Processed by caArray

Investigation Description Format (IDF)

.idf

A 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
titleWarning

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 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.

Data Matrix Raw and processed data files

.txt or other

Contains processed array data files in ASCII or binary files, typically in their native formats; alternatively, data may also be provided in a specially defined MAGE-TAB tab-delimited text format. format termed a "data matrix"

Of data matrix files, only Only copy number data matrix files parsed

In addition to the MAGE-TAB file types described above, the MAGE-TAB specification defines one additional file type to fully describe a microarray investigation: Raw and processed data files – ASCII or binary files, typically in their native formats; alternatively, data may also be provided in a specially defined tab-delimited format termed a "data matrix", described in the table above.

Raw and processed data files – ASCII or binary files, typically in their native formats; alternatively, data may also be provided in a specially defined tab-delimited format termed a "data matrix", described below.

See also About File Types in caArray and MAGE-TAB in caArray--Overview.

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