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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.

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. Processed data can be binary as well, such as Affymetrix MASS generated CHP files.

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