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Affymetrix Power Tools (APT) are a set of cross-platform command line programs that implement algorithms for analyzing and working with Affymetrix GeneChip® arrays. APT is an open-source project licensed under the GNU General Public License (GPL). (Developers who need a non-GPL license may purchase a commercial license from Affymetrix.) APT programs are intended for "power users" who prefer programs that can be utilized in scripting environments and are sophisticated enough to handle the complexity of extra features and functionality. The vision is that APT provides a platform for developing and deploying new algorithms without waiting for the GUI implementations.
Two of the most popular programs and their features are:
- apt-probeset-summarize: An application for analyzing expression (i.e., U133 and Exon Arrays). Features include:
- Multiple summarization methods like PLIER, RMA, MAS5, DABG, and
IterPLIER
- Sketch quantile normalization (saves memory)
- Lots of parameters available to power users
- Save and reuse feature effects and target normalizations
- Use meta-probeset files to group probe sets into larger probe sets
(i.e., combine exons into genes)
- Can run thousands of chips in 1-2 GB of RAM by dividing job into
smaller pieces
- Jobs can be split for running on cluster
- Run multiple analysis at once (i.e., Plier and RMA)
- Relatively fast and robust: process 848 Human Exon Arrays with
RMA-sketch in about two days on Windows 2 GB RAM machine
- See the manual for more details
- apt-probeset-genotype: An application for making genotype calls using Mapping Arrays (100K, 500K, Genome-Wide SNP Arrays 5.0 and 6.0). Features include:
- Implements BRLMM, BRLMM-P and Birdseed algorithm
- Will output DM calls
- Outputs allele summaries for copynumber applications
- Lots of parameters available to power users
- Save and reuse feature effects and target normalizations
- Jobs can be split for running on cluster
- Relatively fast and robust: BRLMM on 96 250K Sty arrays in about
60 minutes on Windows 2 GB RAM machine
- See the manual for more details
More information on APT can be found in the APT documentation included in the APT downloads and available here. APT programs are distributed as Affymetrix Developer Tools (DevNet Tools). According to the Affymetrix support policy
only minimal support is provided. APT does have a community message
board (registration required) where users can post questions/tips
for others.
For more information about the analysis of exon arrays, see the Exon
Array Data Analysis Page. For Expression
Console™ (pgf/clf files for exon arrays) and GCOS
(cdf file for 3' IVT expression arrays) library files and annotations, see
the support page for the specific array of interest. Meta probe set files
are also available on the array support side for performing gene-level signal
summarization using exon arrays.
Parts of the APT package are used by the Expression
Console, Genotyping Console and BRLMM
Analysis Tool applications.
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APT is available as a Windows installer package, pre-built binaries for Linux and Mac OS-X, and as source code. APT versions available for download are listed
below with the most recent release at the top. Note that multiple versions
of APT can be installed simultaneously on the same computer. See the APT Platform page for for more details about compute hardware for running APT.
APT 1.8.6 (Change Log, License)
Older archived versions of APT are available on the APT archive.
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Support for APT is handled through the Affymetrix Developer Network. Questions, problems, feature requests and other issues can be addressed in the APT
User Forum and via the Developer Network email address, devnet@affymetrix.com.
To get email updates about APT or to view previous APT announcements see
the APT
User Forum.
For more general information on support for DevNet tools, see the Software
Support Policy.
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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.
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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.
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