The CEL file preprocessing and the newly added SAM filter utilities require the pre-installation of one of the recent versions of R, a free software environment for statistical computing and graphics. R can be installed from: http://cran.r-project.org/.
Upon the first time that Expander uses R external application, a window will pop, asking you to specify your R software location. Please browse to the location of your R software. In Windows, R.exe file is likely to be located in the 'bin' folder of R software. In Linux, you may type 'which R' in the command line to find R path. If you have a few versions of R installed, please make sure to point Expander to a version in which the necessary packages have been installed.
You may also specify R location from the menu: Options >> Settings >> External applications.
To use R utilities, please make sure there are no white spaces in the path of Expander directory (or the CEL files directory, if loading CEL files). For example, if the name of the Expander folder is 'Expander 5', change it to 'Expander_5'. If Expander is under "Program Files" it should be moved to another location, because of the space between "Program" and "Files". The R software does not cope well with spaces in the path.
Also, please make sure to have 'write' permission to the Expander\Rscripts directory. If you are loading CEL files, check also that you have 'write' permission to the Files location which you specified in the 'Load CEL Files' dialog box.
After specifying R software location, a window will pop, asking you to approve or disapprove automatically installation of R packages when needed.
If you approve automatically installation of R packages then when R utility is used in Expander, Expander will automatically install the needed R packages for the used R utility.
If you disapprove automatically installation of R packages then please refer to "Manually installation of R packages" section.
After installing R, please do the following to install the Bioconductor “affy” package , "gcrma" package and the "samr" package:
1. Run R.
2. In the R frame\window type the text: source("http://bioconductor.org/biocLite.R")
3. Press ‘Enter’.
4. In the R frame\window type the text: biocLite("affy")
5. Press ‘Enter’.
To install the 'samr' package:
6. In the R frame\window type the text: install.packages("samr")
7. R frame\window type the text: install.packages("impute")
8. Press ‘Enter’.
To install the ‘eisa’ package:
9. In the R frame\window type the text: biocLite("eisa")
10. Press ‘Enter’.
To install the 'gcrma' package:
11. In the R frame\window type the text: source("http://bioconductor.org/biocLite.R")
12. Press ‘Enter’. In the R frame\window type the text:
13. biocLite("gcrma")
14. Press ‘Enter’.
You may install only one of the packages, depending on what you wish to use (to install only "samr", follow instructions number 1, 6 and 7).