AffyMAPSDetector Download and Installation

AffyMAPSDetector version 1.0 is now available for download. To install AffyMAPSDetector:

1. Download and save AffyMAPSDetector_v1.zip file.
2. Make sure that you have jre 1.4 or higher version installed. If not, you can download and install jre 1.4 from http://java.sun.com/j2se/.
3. Browse your file system to the location where AffyMapsDetector_v1.zip is saved and use any unzip utility available on your computer system (e.g. winzip on Windows, gunzip/tar on Unix/Linux). Alternatively, if you have jdk1.4 (NOT jre1.4) installed on your machine, then you can use jar utility that comes with it. To use it, open command-prompt (Window users) or terminal/console (Unix/Linux/Mac users); Change directory to the location where AffyMapsDetector_v1.zip is saved and run the command: "jar -xvf AffyMapsDetector_v1.zip". This will create a new directory “AffyMapsDetector_v1” in your current directory.
4. Make sure the directory has following folders and files:
   • sample-data-files
     • HG_U95Av2_gene_info(trimmed).txt
     • HG-U95Av2_probe_tab
   • affymapsdetector.jar
   • commons-math-1.1.jar
   • license.txt
   • log4j-1.2.8.jar
   • README
   • run.bat
   • run.sh
5. Window user can launch AffyMAPSDetector by double clicking on run.bat file. Unix/Linux users can launch it by running the shell script ./run.sh.
6. Read user guide to learn how AffyMAPSDetector works and how to use it. For your convenience, we have also provided GeneChip™ HG-95Av2 “gene information” and “probe information” files in the Supplementary Data section. These files can also be downloaded from www.affymetrix.com/analysis/index.affx which maintains upto date version of these files. For this you may need to open a free account first to access Affymetrix data analysis center (NetAffx^TM). For your convenience, both of these files are also included in the AffyMAPSDetector distribution (see sample-data-files under item #4 above).
7. Note: AffyMAPSDetector has been tested on Window and Linux platforms, however, given Java's platform independence we expect it should work on any other platform. If you have problems, please contact us via email.
8. If you run into memory problem (e.g. if you see java.lang.OutOfMemory error), then do the following:
   • Exit AffyMAPSDetector
   • Open run.bat (on Windows platform) or run.sh (on Unix/Linux platform) and change -Xmx256m to something like -Xmx300m. Make sure that new memory heap size (e.g. 300meg in this case) is less than the physical size of your computer's Random Access Memory (RAM).
   • Save run.bat/run.sh file and close it.
   • Restart AffyMAPSDetector. If you still see memory problems, repeat the above mentioned process.