(Optional) Install R (http://www.r-project.org). R is required for certain modules such as baseline correction or heat maps. The following packages must be installed in your R distribution: rJava, ptw, gplots, xcms and CAMERA. To install them, run the following commands in R:
Edit the startup script in a text editor and adjust the parameters in the script (e.g. HEAP_SIZE or JAVA_COMMAND), if necessary. For integration with R you will need to correctly configure the following:
This is the directory where R is installed, e.g. for Windows it will be something like C:\Program Files\R\R-3.0.3.
This is the directory in which R installs third-party packages. It's usually a subdirectory of your personal directory, e.g. for Windows it will be something like %USERPROFILE%\Documents\R\win-library\3.0.
Append the directory that contains R's libraries. It will be a subdirectory of %R_HOME%, e.g. for 64-bit Windows %R_HOME%\bin\x64 or for 32-bit Windows it will be something like %R_HOME%\bin\i386.
This is the directory where rJava has installed its JRI libraries. It will be a subdirectory of %R_LIBS_USER%, e.g. for 64-bit Windows %R_LIBS_USER%\rJava\jri\x64 or for 32-bit Windows it will be something like %R_LIBS_USER%\rJava\jri\i386.