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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:

    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 from Affymetrix genotyping arrays (Axiom™ genotyping arrays, 100K and 500K mapping arrays, Genome-Wide SNP Arrays 5.0 and 6.0).
    Features include:

    • 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

    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 Axiom™ Analysis Suite, Chromosome Analysis Suite (ChAS), Expression Console™ Software, Genotyping Console™ Software, 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 1.18.2

Change Log | Platforms

File Size md5 Checksum
APT 1.18.2 Source Code 122 MB ad68599e7f20f46ac46d58f4b3006008
APT 1.18.2 Windows Installer - win64 93 MB f91a1989be28d54adf405ed47946b093
APT 1.18.2 Apple Yosemite 64 bit x86 123 MB aa1cd8afc4aec160bc5c9d3fcb0387cb
APT 1.18.2 Linux 64 bit x86 binaries 141 MB 129fdc45af1f8e7fbcaf7436e71bfc18

If you are compiling APT from source code we strongly encourage you to run the regression tests. Regression test data is available as an Amazon Web Services snapshot - search public snapshots for "apt-1.15.2-regression-data", snapshot id snap-d7258dde

The below Affymetrix Power Tools (APT) versions are (OLD) archived versions for your historical use.

APT 1.18.0

Change Log | Platforms

File Size md5 Checksum
APT 1.18.0 Source Code 119 MB 4da8ae2a23274d9fd6f455886fee51fd
APT 1.18.0 Windows Installer - win64 83 MB 8e4faadcb5d06fb4fde8d62482108587
APT 1.18.0 Apple Yosemite 64 bit x86 117 MB 518c3319a7b6bacd94f08b121a1be8cc
APT 1.18.0 Linux 64 bit x86 binaries 121 MB f15b015d48a4138217ebccf0e276952e

APT 1.17.0

Change Log | Platforms

File Size md5 Checksum
APT 1.17.0 Source Code 119 MB 02a77400dd572783c9da48719ba8210f
APT 1.17.0 Windows Installer - win64 80 MB 66274173eeb02d74b56e8a9d751fb435
APT 1.17.0 Linux 64 bit x86 binaries 136 MB 3279f74d03d0d064b671feeefe109fc8
APT 1.17.0 Mac OS-Lion 64-bit Intel Binaries 125 MB 39e836a60a262793423db561cd9c6169

APT 1.16.1

Change Log | Platforms

File Size md5 Checksum
APT 1.16.1 Source Code 119 MB f66649ddfe4d027d9ec16d896dcfddf3
APT 1.16.1 Windows Installer - win64 69 MB f339371b1e0ba0ab8a7ead96f866f4dc
APT 1.16.1 Linux 64 bit x86 binaries 122 MB 6bc0759fff62de870c9691a83942ef48
APT 1.16.1 Mac OS-Lion 64-bit Intel Binaries 109 MB a800b770f1a76899dea9fb94551004ab

APT 1.16.0

Change Log | Platforms

File Size md5 Checksum
APT 1.16.0 Source Code 119 MB 6be504001cddc2b0e9b43d3615d1d204
APT 1.16.0 Windows Installer - win64 69 MB b14747b0542d68a19a59c4886f1e57eb
APT 1.16.0 Linux 64 bit x86 binaries 122 MB e650eee7c39b963c369191b7e302f440
APT 1.16.0 Mac OS-Lion 64-bit Intel Binaries 109 MB 3c28ce84b9aa48924259f608153161cd

APT 1.15.2

Change Log | License

File Size md5 Checksum
APT 1.15.2 Source Code 119 MB 3d42ff729636b1d070aa02896d2ce68d
APT 1.15.2 Windows Installer - win64 60 MB 22bd9594dd641bce0bae5104961b2919
APT 1.15.2 Linux 64 bit x86 binaries 84 MB 56a0cb639f5d6a53a38a13e29324e5b5
APT 1.15.2 Mac OS-Lion 64-bit Intel Binaries 85 MB 162929851c1037b5b152a8a6c8fdfa1e

APT 1.15.0

Change Log | License

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

Change Log | License

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

Change Log | License

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

Change Log | License

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

Change Log | License

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

Change Log | License

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

Change Log | License

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

Change Log | License

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

Change Log | License

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

Change Log | License

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

Change Log | License

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

Change Log | License

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

Change Log | License

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

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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.