Difference between revisions of "R installation"

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Line 18: Line 18:
 
* Agilent normalization (from R-console):
 
* Agilent normalization (from R-console):
 
  biocLite("limma")
 
  biocLite("limma")
*To use BioUML capabilities from R scripts install [[RBioUML]] package:
+
*To use BioUML capabilities from R scripts install [[Rbiouml]] package:
 
  install.packages("rbiouml")
 
  install.packages("rbiouml")
  

Revision as of 09:21, 13 September 2013

This page describes how to install R for BioUML. You need to perform the following steps:

  • R itself:
yum install R

or

apt-get install r-recommended
  • Rserve:
apt-get install r-cran-rserve
  • Set high enough socket connection timeout, add following line to /etc/R/Rprofile.site
options(timeout=864000L);
  • BioConductor (from R-console):
source("http://bioconductor.org/biocLite.R")
biocLite()
biocLite("makecdfenv", lib="/usr/local/lib/R/site-library")
  • Illumina normalization (from R-console):
biocLite("lumi")

Note that this step may require installation of additional packages in the system like libxml2-dev, libglut3-dev, libcurl4-gnutls-dev.

  • Agilent normalization (from R-console):
biocLite("limma")
  • To use BioUML capabilities from R scripts install Rbiouml package:
install.packages("rbiouml")

See also

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