Affymetrix Power Tools (APT) -- Release apt-1.12.0

The Affymetrix Power Tools (APT) is a collection of command line programs for analyzing and working with Affymetrix microarray data. These programs are generally focused on CEL file level analysis. APT also refers to the underlying C++ source code. Binaries and source code are available from the main APT website, http://www.affymetrix.com/support/developer/powertools/index.affx.

Power User Manuals

Power user manuals are available for specific command line applications:

• Main Applications:
  • apt-probeset-summarize: A program for analyzing expression arrays including 3' IVT and exon arrays. Supports background correction (MAS5,RMA), normalization (linear scaling, quantile, sketch), and summarization (PLIER, RMA, MAS5) methods.
  • apt-probeset-genotype: A program for analyzing mapping arrays. Supports BRLMM-P, Birdseed, and BRLMM methods for genotype calling.
  • apt-geno-qc: A program for doing single chip QC of WGSA genotyping arrays.
  • apt-copynumber-workflow: A program to run the copy number analysis workflow on SNP6 arrays.
    • apt-copynumber-reference: A program to run the reference building portion of the copy number analysis workflow on SNP6 arrays. Most users will probably want to use apt-copynumber-workflow rather than this program.
    • apt-copynumber-log2ratio: A program to run the log2ratio portion of the copy number analysis workflow on SNP6 arrays. Most users will probably want to use apt-copynumber-workflow rather than this program.
    • apt-copynumber-analysis: A program to run the various CN analysis methods (ie LOH, CN HMM, ...) portion of the copy number analysis workflow on SNP6 arrays. Most users will probably want to use apt-copynumber-workflow rather than this program.
  • apt-canary: A program to compute copy number variation calls given a known set of CNV regions.
  • apt-dmet-genotype: A program to compute genotypes and copy number variation from DMET Plus CEL files. DMET CHP files are generated.
  • apt-dmet-translation: A program to compute star allele translation reports from DMET Plus CHP files.
• Utility Programs:
  • apt-cel-transformer: A program for applying arbitrary chipstream methods (ie quantile normalization, RMA background correction) to a set of cel files, resulting in a new set of cel files.
  • apt-cel-extract: A program for extracting feature level intensities from CEL files.
  • apt-cel-convert: A program for converting CEL files to different formats.
  • apt-chp-to-txt: A program to dump AGCC and XDA chp files as text.
  • apt-file5-util: A program to convert between a5 and text formats.
  • apt-engine-wrapper: A program to directly call analysis engines. The main use is to run it with the help option in order to find out what options various sub-engines will except.
  • apt-summary-genotype: A program to run BRLMM-P family of algorithms on allele summaries.
• Legacy Programs (likely to be removed in later APT releases):
  • apt-dump-pgf: A program for extracting chip layout information from PGF and CLF files.
  • apt-midas: A program to compute MiDAS (alternative splice detection) scores from exon array results.
  • apt-summary-vis: A program to generate IGB visualization files (EGR) and Wiggle visualization files from apt-probeset-summarize summary files
  • apt-tsv-join: A program to merge TSV and CSV files (ie summary and annotation files).

More Detailed Documentation

For specific details see:

• index.html: This document
• INSTALL.html: Notes on how to install APT
• CHANGE.html: Specific changes associated with each release version
• VIGNETTE.html: List of vignettes available for APT. Vignettes are brief and concise documents on specific topics.
• FAQ.html: List of FAQs pertaining to the whole of APT. Program and application FAQ items are listed in program manuals and application vignettes.
• FILE-FORMATS.html: Information about file formats used by APT.

History and Changes

The APT code provides the back end analysis engine for Expression Console and Genotype Console. The APT packaged evolved out of an early exon array analysis package called ExACT. All users should review the Change Log for details on changes made to APT. Changes to algorithm behavior and the addition of new features will be itemized in the Change Log. The latest information and downloads for APT are available on the APT DevNet website.

Compute Platforms

See the Platforms page for more information.

License

See the License page.

Support

Support for APT is handled through the Affymetrix Developer Network. Specifically, questions, problems, feature requests, and other inquiries should be made through either the APT User Form or the Developer Network email address, devnet@affymetrix.com. (If you get an Internal Server Error when accessing the forum, try clearing your cookies for affymetrix.com.) To get emails updates about APT or to view previous APT announcements see the APT User Form.

APT is not supported through the Affymetrix call center, Field Application Specialists, or other standard Affymetrix Technical Support channels.

NO WARRANTY

THE PROGRAM IS PROVIDED ON AN "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, EITHER EXPRESS OR IMPLIED INCLUDING, WITHOUT LIMITATION, ANY WARRANTIES OR CONDITIONS OF TITLE, NON-INFRINGEMENT, MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. Each Recipient is solely responsible for determining the appropriateness of using and distributing the Program and assumes all risks associated with its exercise of rights under this Agreement, including but not limited to the risks and costs of program errors, compliance with applicable laws, damage to or loss of data, programs or equipment, and unavailability or interruption of operations.

DISCLAIMER OF LIABILITY

NEITHER RECIPIENT NOR ANY CONTRIBUTORS SHALL HAVE ANY LIABILITY FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING WITHOUT LIMITATION LOST PROFITS), HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OR DISTRIBUTION OF THE PROGRAM OR THE EXERCISE OF ANY RIGHTS GRANTED HEREUNDER, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.

Affymetrix Power Tools (APT) Release apt-1.12.0