File Formats

• GCOS and AGCC Formats
  • CDF: Chip layout information. What probes are where on the chip and how are they grouped into probesets.
  • CEL: Probe level intensity data on a per-chip basis.
  • CHP: Probeset summary information (ie probeset signal, genotype calls, ...) on a per chip basis.

• Tab-Separated Values file: TSV is a general file format for textual information.
  • Version 1 TSV (normal)
    • BGP: BackGround Probes file: The BGP file lists what probes (by probe ID) are to be used in various generic background correction methods (ie GCBG method).
    • CLF: CEL Layout File: CLF along with PGF make up the core chip layout information for WT-based expression designs (Gene and Exon arrays). The CLF contains the mapping of probe IDs to x/y positions in the CEL file. Note that this mapping may be deterministic based on CLF header info.
    • CSV: Comma-Separated Values file: The CSV is a general file format for textual information. While not strictly a "TSV" file, it is placed in the TSV family due to the use of the TsvFile parser to handle these files.
    • GQC: Genotype Quality Control File: The GQC file contains quality assessment metrics for genotyping arrays.
    • MPS: Meta Probeset File: The MPS file is used to group individual probesets into a meta probesets. This is most commonly used on the WT-Based expression platform to group exon level probesets into a gene level meta probeset.
    • PS: Probeset List File: The PS file is used to provide a list of probeset IDs or names.
    • QCA: Quality Control Analysis File: The QCA file is used to define quality assessment analysis methods for genotyping arrays.
    • QCC: Quality Control Content File: The QCC file is used to define quality assessment groupings, textual labels, amongst other things for genotyping and expression arrays.
    • SPF: Simple Probe File: The SPF is an experimental format for specifying probe layout information.
  • Version 2 (hierarchical)
    • Probe Group File (PGF): PGF along with CLF make up the core chip layout information for WT-based expression designs (Gene and Exon arrays). The PGF groups specific probes (by probe ID) into probe sets.

• HDF5 (a5) file: HDF5 is a binary file format.
  • Copynumber Reference format (REF)
    • REF: CN5 Reference file: Copynumber Reference format (REF) is a hdf5 binary representation of the data needed to run the copynumber single sample workflow.

Affymetrix Power Tools (APT) Release apt-1.10.1

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