Affymetrix Power Tools (APT)
Overview
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.
Restrictions on use
All users may access and use APT.
Running the application
Please do not run APT commands on the login node. qrsh is recommended for some commands. Computationally intense work should be done via the batch system.
Examples
The following example first runs apt as a serial job.
#!/bin/bash --login #SBATCH -p serial # (or --partition=) Use the nodes dedicated to 1-core jobs #SBATCH -t 4-0 # Wallclock limit of 4 days. Max permitted is 7-0. module purge module load apps/binapps/apt/2.11.0 apt-probeset-summarize -a rma-sketch -a plier-mm-sketch -p chip.pgf -c chip.clf -o output-dir *.cel
and submit the job using qsub jobscript where jobscript is the name of your job script file.