An Array Description Format (ADF) file is a tab-delimited file that describes the design of an array, for example, the sequence of the probe located at each position on an array and the annotation of this sequence. If the investigation uses arrays for which a description has been previously provided, such as a standard commercial array, cross-references to entries in a public repository (for example, an ArrayExpress accession number) can be included instead of explicit array descriptions.
GCCs submit ADF files to the DCC only if the platform used is non-standard. For example, if a GCC uses the Affymetrix HT_HG-U133A array, a well-known standard platform, it does not submit an ADF file. If a GCC uses a non-standard platform to derive methylation data, it submits an ADF along with the other corresponding data. The following figure shows an example of a simple ADF file from the MAGE-TAB specification document.
ADF files should be provided for non-standard array designs (e.g. Illumina) or complex designs where additional metadata can be provided (e.g. Affymetrix Exon 1ST). In those cases, transfer a standardized ADF file in your first archive only. In all subsequent archives, place a blank dummy file with the same ADF file name in your archive as a placeholder. That will ensure that your archive is valid. The DCC will ensure that your archives are linked to the original ADF file. If you do include an ADF file, you should list the ADF file name in the "Array Design File" column and list your "Array Design REF" name.
Array Design REF
The "Array Design REF" column in the SDRF file is used to reference an Array Design File available via the Web. Although "Array Design REF" names are self-assigned, you should follow the prescribed scheme below and those names should persist unless the Array Design changes. The format of that name should be:
- VendorDomain should match your vendor's Internet domain name (e.g. Agilent.com).
- PhysicalArrayDesign is an MGED Ontology term and should be entered verbatim.
- PlatformCode, when possible, should match your vendor's code (e.g. HG-U133_Plus_2) for the platform you are using. In instances where your vendor does not provide that type of code, terse yet descriptive abbreviated words can be used. Chip sets that are different in design (e.g. Affymetrix 500K Set) should be named differently. In cases where the code is too generic (e.g. 550K), the code should be concatenated with the vendor's abbreviated name (e.g. Illum550K). More information on different platforms and associated codes can be found in the Platform topic.
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