R installation

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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")

See also

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