The GeneSpring GX R-integration package will allow you to expand the capability of GeneSpring by integrating R programs seamlessly into GeneSpring. With the integration package you will be able to use the power of R and BioConductor scripts in GeneSpring's rich graphical environment.
Last update: 27-Jun-2005 A new version of the R-integration package was released 27-Jun-2005. The new features of the release include:
- Upgrade R to version 2.1.0 - The version of R that is included in this release is version 2.1.0, released 18-Apr-2005. This contains numerous changes and bug fixes. For a complete list of the new features in R 2.1.0 consult the R web site.
- Added box plot script - Added new example script to create a simple Box Plot in R.
- Removed RMA scripts - Since GeneSpring GX 7.1 has native support for RMA and GC-RMA analysis of CEL files, there is no need for a R version of the RMA scripts and therefore have been removed from this version.
- All of the scripts were updated to work with GeneSpring GX R library version 2.0.0 - BioConductor 1.6 contains a new version of the GeneSpring GX library (version 2.0.0) and the example scripts were changed to work with GeneSpring GX library version 2.0.0.
GeneSpring GX library version 1.0.x used the GeneSpring GX systematic name as row names for many of the expression matrices and certain characters that are valid characters in systematic names (Namely #) are not valid characters for Matrix row names, leading to some conversion issues. GeneSpring GX library 2.0.0 stores the gene names in a special slot, allowing for any character to be used as a systematic name.
NOTE: R scripts written to use GeneSpring GX library 1.0.x ARE NOT COMPATIBLE with this new version of the GeneSpring GX library.
- All of the scripts were updated to work with R version 2.1. - The contents of certain libraries have been changed in R version 2.1.0 and the example R scripts have all been updated to work with R version 2.1.
The installation package will install R and a number of examples to help you create your own library of R scripts.
For those who already have a copy of R, we have provided an installer that only contains the GeneSpring-specific part of the R integration package. This version may require you to edit two files to indicate the path to the R program. For more information on the installation procedure see the GeneSpring-R Integration Package PDF document.
If you are using a Windows system and don't have R and/or BioConductor installed, download the following package:
WINDOWS including R program (2.1.0) and BioConductor (1.6) + GeneSpring library (2.0.0).
Drop the ZIP file you get onto any open window of GeneSpring and this will install everything.
For those who either already have R and/or BioConductor, or want to install R onto a Macintosh or other UNIX system, install the R-integration package follow these steps below:
- Download and install R version 2.1.0 from: http://cran.us.r-project.org/
- Download and install the BioConductor R (version 1.6) libraries from: http://www.bioconductor.org/
Installation of the BioConductor libraries is done within the R program. See the installation instructions on the website. The minimum required libraries for implementing the R integration package are the BioBase and GeneSpring libraries.
- Download and install the GeneSpring-R Integration package ZIP file from our web site.
WINDOWS without the R program or any library
UNIX without the R program or any library
Drag the ZIP file onto any open window of GeneSpring or use Menu File › Open GeneSpring Zip
- Change the path for the scripts and/or R program (See section 3.3 of the GeneSpring-R Integration Package PDF)
- Change the permission on the execution scripts (UNIX only, See section 3.3.2)
- PRESTO! You are done… It's that simple to get started with R in GeneSpring!
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