Affymetrix Power Tools (APT) Software Package
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:
- 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
- Implements Axiom™ genotype caller, Birdseed, BRLMM-P, and BRLMM algorithms
- Axiom™ Genotyping Solution Data Analysis Guide (pdf, 3 MB)
- 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
apt-probeset-summarize: An application for analyzing expression (i.e., U133 and Exon Arrays).
Features include:
apt-probeset-genotype: An application for making genotype calls from Affymetrix genotyping arrays (Axiom™ genotyping arrays, 100K and 500K mapping arrays, Genome-Wide SNP Arrays 5.0 and 6.0).
Features include:
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.
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 AGCC (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 Chromosome Analysis Suite (ChAS), Expression Console, Genotyping Console and BRLMM Analysis Tool applications.
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 1.15.1
| File | Size | md5 Checksum |
|---|---|---|
| APT 1.15.1 Source Code | 119 MB | c2811a10cc920b8815b45c1d2252c617 |
| APT 1.15.1 Windows Installer - win64 | 60 MB | d78993dc4affa2dc69e907be05e9176c |
| APT 1.15.1 Linux 64 bit x86 binaries | 84 MB | 65846a06268e0125bbeabba241d69e75 |
| APT 1.15.1 Mac OS-Lion 64-bit Intel Binaries | 85 MB | e606cc153d679032e1e12c222898c484 |
If you are compiling APT from source code we strongly encourage you to run the regression tests. Regression test data is available at: https://bioinfo.affymetrix.com/APT/, or as an Amazon Web Services snapshot – search public snapshots for "apt-1.15.1-regression-data", snapshot id snap-d7258dde
The below Affymetrix Power Tools (APT) versions are (OLD) archived versions for your historical use.
APT 1.15.1
| File | Size | md5 Checksum |
|---|---|---|
| APT 1.15.1 Source Code | 119 MB | c2811a10cc920b8815b45c1d2252c617 |
| APT 1.15.1 Windows Installer - win64 | 60 MB | d78993dc4affa2dc69e907be05e9176c |
| APT 1.15.1 Linux 64 bit x86 binaries | 84 MB | 65846a06268e0125bbeabba241d69e75 |
| APT 1.15.1 Mac OS-Lion 64-bit Intel Binaries | 85 MB | e606cc153d679032e1e12c222898c484 |
If you are compiling APT from source code we strongly encourage you to run the regression tests. Regression test data is available at: https://bioinfo.affymetrix.com/APT/, or as an Amazon Web Services snapshot – search public snapshots for "apt-1.15.1-regression-data", snapshot id snap-d7258dde
APT 1.15.0
| File | Size | md5 Checksum |
|---|---|---|
| APT 1.15.0 Source Code | 120 MB | c977a62ae980b94e20544c3dba0c6ed6 |
| APT 1.15.0 Windows Installer - win64 | 48 MB | 0db0bf18b792cae5fe394bd16a41aa27 |
| APT 1.15.0 Linux AMD 64 bit binaries | 85 MB | 199eaa4d090fed47aa6959bd5c30ba4d |
| APT 1.15.0 Mac OS-Lion 64-bit Intel Binaries | 86 MB | 75400218cb982b7015a46ac282008c06 |
APT 1.14.4.1.1
| File | Size | md5 Checksum |
|---|---|---|
| APT 1.14.4.1 Source Code | 118 MB | 256327f65fc35bede0dd7880ddd830d3 |
| APT 1.14.4.1 Windows Installer - win64 | 62 MB | 17d828217c4905809a3ba854a3d89306 |
| APT 1.14.4.1 Linux AMD 64 bit binaries | 80 MB | 0b44a556f57f83a5affbca901f599881 |
| APT 1.14.4.1 Mac OS-Lion 64-bit Intel Binaries | 81 MB | 311fa079d8ee5ec3f22cb1e0b5a75924 |
APT 1.14.3
| File | Size | md5 Checksum |
|---|---|---|
| APT 1.14.3 Source Code | 118 MB | 06a41853fd4955e511f32f7b5e8cd029 |
| APT 1.14.3 Windows Installer - win64 | 62 MB | 6BECF4B67B5C3FDD16DC164880B9FE68 |
| APT 1.14.3 Linux AMD 64 bit binaries | 80 MB | d0b0ec7e5ded9530c58f30293429ac7f |
| APT 1.14.3 Mac OS-Snowleopard 64-bit Intel Binaries | 83 MB | b82e28ff5afcbb543d8ed50633a1483a |
APT 1.14.2
| File | Size | md5 Checksum |
|---|---|---|
| APT 1.14.2.1 Source Code | 118 MB | ddc28d28e8c5cb648eadd453f2797ab |
| APT 1.14.2 Windows Installer - win32 | 34 MB | d2bfc8ce8e2a993b6201bb7ac543660d |
| APT 1.14.2 Windows Installer - win64 | 64 MB | 4f12d6907f7b857e2ffe8b5244bd4c4c |
| APT 1.14.2 Linux i386 32 bit binaries | 87 MB | a0514ceb7dab4ed9ad43b0f3b5d33b6c |
| APT 1.14.2 Linux AMD 64 bit binaries | 84 MB | a3d3b7b310cc9c70bacb49560d646db7 |
| APT 1.14.2 Mac OS-Snowleopard 64-bit Intel Binaries | 87 MB | 3e3847572345a4f483132e235a95ad42 |
APT 1.12.0
| File | Size | md5 Checksum |
|---|---|---|
| APT 1.12.0 Source Code | 125 MB | 16623c5c6e327b5bdadeb81e7b3bc8d7 |
| APT 1.12.0 Windows Installer - win32 | 53.1 MB | b95558fa51d49f611b38fa3c43726f19 |
| APT 1.12.0 Windows Installer - win64 | 129 MB | bd2cdb3dcf92178f24ce934678f22e0c |
| APT 1.12.0 Linux i386 32 bit binaries | 104 MB | 09975b48beff4a675f427d9a36977c75 |
| APT 1.12.0 Linux AMD 64 bit binaries | 107 MB | 46e90ec1f4cc0b7fec9ae1b5bddefcbb |
| APT 1.12.0 Mac OS-X Tiger (10.4) 64-bit Intel Binaries | 81.8 MB | e5ac9b0c6b40e3a625c4a7678684891d |
APT 1.10.2
| File | Size | md5 Checksum |
|---|---|---|
| APT 1.10.2 Source Code | 94.3 MB | 8a6844ed70723a4a7c671a4da69a45c8 |
| APT 1.10.2 Windows Installer - win32 | 90.4 MB | c2c69d0d4fa90a35e5e0ad1fde6f55a3 |
| APT 1.10.2 Windows Installer - win64 | 106 MB | ba6e3693ae05d1fd957f92506fd804f5 |
| APT 1.10.2 Linux i386 32 bit binaries | 77.7 MB | 30f5e3ff7223250bb927838375f37aec |
| APT 1.10.2 Linux AMD 64 bit binaries | 79.7 MB | 20a3a89e590deb8953d932df868bafbb |
| APT 1.10.2 Mac OS-X Tiger (10.4) 64-bit PowerPC Binaries | 18.2 MB | c6fdcf708aaeeafd2aab1b38b6ac6a19 |
| APT 1.10.2 Mac OS-X Tiger (10.4) 64-bit Intel Binaries | 59.1 MB | b9dc6569fbeae0d7c399d57901a78019 |
APT 1.10.1
| File | Size | md5 Checksum |
|---|---|---|
| APT 1.10.1 Source Code | 85 MB | 534925916ee0a91975f7b5cb267315ed |
| APT 1.10.1 Windows Installer - win32 | 61.8 MB | de363563e89a28f1de3b7f0018fe5b32 |
| APT 1.10.1 Windows Installer - win64 | 74.6 MB | ae3b112e6b417b26fdfc542c51b56ee7 |
| APT 1.10.1 Linux i386 32 bit binaries | 65.0 MB | ed7db6d05c57b3b1ecc9daf712f48c49 |
| APT 1.10.1 Linux AMD 64 bit binaries | 31.7 MB | 65796f0a8f4a38aca4ee74c355e2bbea |
| APT 1.10.1 Mac OS-X Tiger (10.4) Universal Binaries (Not Tested!) | 72.8 MB | f2b4a3e428745eac3e803f1980fca189 |
| APT 1.10.1 Mac OS-X Tiger (10.4) i386 Binaries | 53.1 MB | 178e423ab4cc6f8604f302283953e877 |
APT 1.10.0
| File | Size | md5 Checksum |
|---|---|---|
| APT 1.10.0 Source Code | 75.7 MB | 1dd19db801b0d20de427ae5c21dc940d |
| APT 1.10.0 Windows Installer - win32 | 26.8 MB | 605a0e4c9e0759ee3b8a306f3a8b5b7c |
| APT 1.10.0 Windows Installer - win64 | 30.8 MB | a2dfd8e41d5af2300bdcbc6f2246cfd9 |
| APT 1.10.0 Linux i386 32 bit binaries | 30.2 MB | 67fcb18fb16b205b85a6905c07783521 |
| APT 1.10.0 Linux AMD 64 bit binaries | 31.7 MB | bd908eb7beff73264774012ceaa72352 |
| APT 1.10.0 Mac OS-X Tiger (10.4) ppc Binaries | 18.2 MB | e0c22df17d64d82956631131df0ae7b1 |
| APT 1.10.0 Mac OS-X Tiger (10.4) Universal Binaries (Not Tested!) | 72.8 MB | fd29f50dada58af453072ef2c73fc7d2 |
| APT 1.10.0 Mac OS-X Tiger (10.4) i386 Binaries | 19.2 MB | 3424e854abba2aadb0c5d72e0d35af21 |
| APT 1.10.0 Sparc Sun Solaris Binaries | 27.3 MB | 6e22f71522a3ae687020203f90e3a5c4 |
APT 1.8.6
| File | Size | md5 Checksum |
|---|---|---|
| APT 1.8.6 Source Code | 28 MB | 92ea3f9ce47d8b45556605242f7a55b2 |
| APT 1.8.6 Windows Installer - win32 | 19.4 MB | 7097e9db31b7099babb504efb7d06f07 |
| APT 1.8.6 Windows Installer - win64 | 22.5 MB | 248350cc909d9ce3eb8aa91a7454f38c |
| APT 1.8.6 Linux i386 32 bit binaries | 18.2 MB | 6920d688135b8c02100868bf5a33bfdc |
| APT 1.8.6 Linux AMD 64 bit binaries | 19.1 MB | e27b781aba722c3b12cd5df3c155f2f3 |
| APT 1.8.6 Mac OS-X Tiger (10.4) ppc Binaries | 8.52 MB | ad40cdf55c22229a1f7d6b1fb88cddf7 |
| APT 1.8.6 Mac OS-X Tiger (10.4) Universal Binaries (Not Tested!) | 34.4 MB | dbc9040c55abbee1d45e892371650a03 |
| APT 1.8.6 Mac OS-X Tiger (10.4) i386 Binaries | 9.23 MB | 069576f1f96a330394248d491f9f40b8 |
| APT 1.8.6 Sparc Sun Solaris Binaries | 14 MB | a1a9958498bdaed74e0a3c614ce05ff7 |
APT 1.8.5
| File | Size | md5 Checksum |
|---|---|---|
| APT 1.8.5 Source Code | 19 MB | 93646226a463d2cd1d9d727e1bc8e490 |
| APT 1.8.5 Windows Installer - win32 | 18.3 MB | ae494265e88b4c5ac24d1491b403c9e2 |
| APT 1.8.5 Windows Installer - win64 | 21.4 MB | 1ceea0672ecf02dd25d86ba23f2eb8f4 |
| APT 1.8.5 Linux i386 32 bit binaries | 15 MB | 1ad150b7fd232757174cfb3c32c46725 |
| APT 1.8.5 Linux AMD 64 bit binaries | 15.7 MB | bf5f0f5157483af7d19ed4025c009185 |
| APT 1.8.5 Mac OS-X Tiger (10.4) ppc Binaries | 6.53 MB | 1ebabc4037e5015910a386f5fcf47744 |
| APT 1.8.5 Mac OS-X Tiger (10.4) i386 Binaries | 6.87 MB | d06e90ae34c438432dbd2f711229885a |
| APT 1.8.5 Sparc Sun Solaris Binaries | 11 MB | f5408bdae50f2ff3323b9538e5d48e10 |
APT 1.8.0
Several issues have been observed with the recent 1.8.0 release of APT. Specifically:
- The txt output (--txt-output option) from apt-probeset-genotype will report forced calls when doing a birdseed analysis, as opposed to applying a confidence-score cutoff to produce no-calls for uncertain genotypes. A future release of APT will phase out the --txt-output option. It is recommended that you use the table text output (--table-output) or AGCC CHP file output (--cc-chp-output). Note that the table output is enabled by default.
- When using the force option (--force) with apt-probeset-genotype, the "Chip Type" field in the resulting CHP files will be empty. The result is CHP files which most applications will be unable to load, including Genotyping Console. A future release of APT will report the CDF Chip Type in the CHP file output.
- The current implementation of birdseed will generate incorrect answers on Solaris-Sparc. Because of this, no Solaris-Sparc binaries were provided. Users compiling APT from source code on Solaris-Sparc machines should note that they should not use their binaries to generate birdseed results.
We anticipate correcting these in the next APT release.
| File | Size | md5 Checksum |
|---|---|---|
| APT 1.8.0 Source Code | 29 MB | 37cce53525130e5c74b3ab449378fff9 |
| APT 1.8.0 Windows Installer | 15 MB | 6e24bc40b8e93e7aab5721b490ef1314 |
| APT 1.8.0 Linux i386 32 bit binaries | 12 MB | 37e5c4609eb909264722c11126145367 |
| APT 1.8.0 Linux AMD 64 bit binaries | 123 MB | 82d117cfcab922fd02bde204cde4a314a |
| APT 1.8.0 Mac OS-X Tiger (10.4) ppc Binaries | 4.8 MB | 41ab75f3018ac2f2668044c481ff182c |
| APT 1.8.0 Mac OS-X Tiger (10.4) i386 Binaries | 5.1 MB | 351c35e28ed8347765da8e5f059ca52e |
APT 1.6.0
| File | Size | md5 Checksum |
|---|---|---|
| APT 1.6.0 Source Code | 23.3 MB | 873b72fd395d5fc5b41652f9bc156841 |
| APT 1.6.0 Windows Installer | 12.5 MB | ffc135d0cac31c42301eccd3c1e44a00 |
| APT 1.6.0 Linux i386 32 bit binaries | 9.7 MB | a060e49b8982b86c3ff10d6e739e900e |
| APT 1.6.0 Linux AMD 64 bit binaries | 11.3 MB | f4c3cbb179fbe344c76fd2e7947f061a |
| APT 1.6.0 Mac OS-X Tiger (10.4) ppc Binaries | 3.7 MB | 0aead873874e2f19e8cca0838baa3c90 |
| APT 1.6.0 Mac OS-X Tiger (10.4) i386 Binaries | 3.8 MB | 0ded8679ef710dc55d83c93b62293bde |
| APT 1.6.0 Sparc Sun Solaris Binaries | 4.9 MB | d10e2335eba0831d701ec4d6f5515f96 |
APT 1.4.0
| File | Size | md5 Checksum |
|---|---|---|
| APT 1.4.0 Source Code | 14 MB | 8926a1688ccc43992e91a8e1b2f74e54 |
| APT 1.4.0 Windows Installer | 9.7 MB | ab9abcdc3a708dc5a3153d1663e6cc48 |
| APT 1.4.0 Linux i386 32 bit binaries | 4.3 MB | c7ff1f250ffc4afb9ea71e7379ba6f22 |
| APT 1.4.0 Linux AMD 64 bit binaries | 5 MB | 03964b5475da8ae0a36bf69fb0ea9e7f |
| APT 1.4.0 Mac OS-X Tiger (10.4) ppc/ppc64/i386 Binaries | 6.6 MB | a4adf5e43f742e1976a37181ba46ba51 |
Support for APT is handled through the Affymetrix Developer Network. Questions, problems, feature requests and other issues can be addressed 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.
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.