Statistics for Bioinformatics
Some chapters of these practicals require the installation of R
librairies. The installation of these librairies is fairly simple, it
can be done by running a few commands from the R application
Practicals - R librairies
For this, you need a HTTP connection. If you are behind a firewall,
you need to define the environment variable http_proxy as explained in
the chapter on configuration.
Note: if you installed the R application as super-user, you
need to run it as super-user in order to install additional packages.
Installing R packages
The R base application includes most of the facilities for classical
statistics. In addition, a large collection of libraries are
available, and can be installed from the application itself. We
illustrate this by installing the library "mda" (mixture and flexible
Open an R application, and run the following commands.
You can now check the installation by loading the library.
If the installation was correct, this command should not return any
message. You can now call the functions from this library, and the
associated help texts. for example, you can call the help for
mda, the method of mixture discriminant analysis.
For the analysis of microarray data, we will use the Bioconductor
package. The installation of this package is slightly different than
for other R librairies, but it is very easy (a two-line
Beware: Bioconductor requires a lot of disk space (170
Mb in the current version), and takes a while (2 hours for downloading
and compiling all the packages). You should thus better prepare this
Mac OSX environment
If you are running R in the Raqua interface, you should
better use the pre-defined command in the menu
Packages > Bioconductor > Download all
Unix and Windows environments
For Unix and Windows environment, the installation of Bioconductor
execute the following steps
- Make sure you have enough disk space (~200Mb) and time before you (2 hours).
- Start an R application.
- Load the installation script from the web site.
- Start the installation.
Jacques van Helden (firstname.lastname@example.org)