A couple of points.  I don't know which Linux distro you are using, but in
general I think it best to install R from the terminal using a CRAN mirror
rather than from the Linux distro repository.  The distro repositories are
sometimes not completely up to date, so you will get more current updates
from the CRAN repositories.  You will also need to add your CRAN mirror to
the Linux software source so it will automatically check for updates.
Instructions for all of this are on the Internet.  When you add new
packages, also use the terminal and log on as an administrative user.
Otherwise, your new packages may not install to the secure system area.

In Linux, the default is for R to run as a terminal application, so you
will need a GUI.  I use R Commander and it works nicely.  It is my
understanding that for some of the more complex analyses it may be best to
use the terminal.  I had a little trouble customizing my R Commander,
especially the font sizes.  This was a bug that was fixed within 24 hours
and now all is good.  An easy way to keep custom settings is with a
.Rprofile file in your user area.  You will also probably want to create a
desktop launcher.

GUI compatibility shouldn't be a problem.  Unlike Windows, in Linux the GUI
is layered on top of the OS.  So, if you use a gnome desktop and want to
run a KDE GUI, it is just a matter of downloading the necessary packages
specific to the GUI.  Linux usually analyzes dependencies and will download
what you need.  One exception i ran into was with the rgl package in R
Commander.  However, a thread on the Ubuntu site provided information about
the missing packages and, once they were installed, all worked well.

Hopefully, you shouldn't have any problems with either a gnome or KDE
desktop.  I can't be so sure about the Unity desktop that Ubuntu has
adopted.  I know, for example, that there have been issues with swt/Jface
Java applications on Unity.  That's why I switched to Linux Mint.

Hope that helps.

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