Affymetrix Power Tools (APT) is a set of cross-platform command line programs that implement algorithms for analyzing and working with GeneChip™ arrays. 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.
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
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
- 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
Axiom Genotyping Solution Data Analysis Guide.pdf
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 support policy below 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.
Download
APT is available as a Windows installer package, pre-built binaries for Linux and Mac OS-X. 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.
