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File Type

File Extension

Description

Processed by caArray

Investigation Description Format (IDF)

.idf

A MAGE-TAB 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 MAGE-TAB 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.

Raw and processed data files

.txt or other

Raw data files: ASCII or binary files, typically in their native formats. Processed (derived) data: tab-delimited text format; can be MAGE-TAB data matrix files.

Of data matrix files, only copy number data matrix files are parsed.

You To load an experiment into caArray using the MAGE-TAB format, you must create the first three two file types, IDF , SDRF and Array Design for your experimentand SDRF. See #Building Building MAGE-TAB Formatted Files for details on making IDF and SDRF files. You also need to make sure that the corresponding Array Design (the third file type) for your experiment has been loaded into caArray. The fourth file type, raw and/or derived (processed) data files are created by the instruments reading the array results.

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