R Integration Setup

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There are a few steps you'll need to perform in order to use the R integration functions of geWorkbench. Note the following instructions are for windows (along with the Rserve.exe) mentioned, but there are similar ways to get this working on other platforms. They are:

  1. Download and install R and Biocontductor - http://bioconductor.org/download
  2. Download an install RServe from http://rosuda.org/Rserve/ - it's important to match the version of RServe to your version of R
  3. Run the Rserve.exe from this folder, it's usually best to run it from the command prompt so you can stop and start it.
  4. Now you can use the R integration in geWorkbench. For example, when opening a file you can use the "GCRMA via R" file loading type and select CEL files for processing in GCRMA.
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