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To participate in the JSM2005 Analysis of Gene Expression Data Workshop, you are expected to have installed R 2.1.1 or R 2.1.0 on your computer beforehand (preferably R 2.1.1). All of the lab exercises can be done on a computer with 512 MB of RAM (or more), and some of them can be done with as little as 256 MB. Before installing R and the required R packages, you should ensure that you have at least 500 MB of free hard disk space. The installation of this software will not require that much space, but whenever installing large software bundles you should allow for some extra space because filling up your hard disk completely can lead to serious performance problems. If you have an existing R installation, you do not need to replace it if you don't want to. You can install the new version of R in a different directory.
This webpage gives a list of the R packages required for the JSM2005 Microarray workshop. You may also wish to check each individual lab page to find out which R packages are required for that particular lab.
If possible, all of these R packages should be installed on your laptop before the workshop. If you are missing any R packages, CDs will be available at the workshop, but there will be no Internet access.
The R_JSM2005 Windows installation wizard below will appear identical to the regular R-for-Windows installation wizard (except much larger). Just install it as you would normally install R, and you will (hopefully) get all of the R packages required for JSM2005 plus the Tcl/Tk extensions required for limmaGUI. The R packages included in this wizard are listed individually in the following section.
If you want to run limmaGUI (highly recommended for Lab 1) and/or affylmGUI, you will need the Tcl/Tk extensions Tktable and BWidget.
If you are using Windows, then you can install ActiveTcl
from :
http://www.ActiveState.com/ActiveTcl
and then limmaGUI and affylmGUI will automatically determine where ActiveTcl
has been installed by looking in the Windows Registry.
Alternatively, you can just use the minimal version of Tcl/Tk distributed in the JSM2005 R for Windows Installation Wizard described in Section 2 which includes the Tktable and BWidget Tcl/Tk packages required by limmaGUI.
The two Tcl/Tk extensions required by limmaGUI (Tktable and BWidget)
can be installed in /usr/local/lib/ or /usr/lib/
or anywhere else within the R-Tcl/Tk search path.
To see your current R-Tcl/Tk search path from within R, type:
library(tcltk)
tclvalue("auto_path")
To add a new directory to the R-Tcl/Tk search path, you can use:
library(tcltk)
addTclPath("/custom/TclTk/path")
To test whether the Tcl/Tk extensions Tktable and BWidget can be found within the R-Tcl/Tk search path, type:
library(tcltk)
tclRequire("Tktable")
tclRequire("BWidget")
For Linux/Unix operating systems, you can download the source of these two Tcl/Tk extensions from:
| Package | URL |
|---|---|
| Tktable | http://tktable.sourceforge.net/ |
| BWidget | http://tcllib.sourceforge.net/ |
From each of the sourceforge websites above, click on "File
Distributions" to download Tktable2.9.tar.gz and
BWidget-1.7.0.tar.gz.
The Tktable package is a standard Linux/Unix source package so
it can be unzipped with tar zxvf and installed with
./configure; make; make install assuming that you have the
appropriate tcl-devel and tk-devel RPMs or that you
have the Tcl/Tk source (from http://www.tcl.tk/). Note that R on Linux/Unix is
generally configured to run with Tcl/Tk 8.3.x, i.e. the version which comes with
most Linux distributions, so if you are installing extensions (e.g.
Tktable), they should be built with Tcl/Tk 8.3.x, rather than
Tcl/Tk 8.4.x. Generally this won't be a problem if you build Tktable
from source using tcl-devel and tk-devel RPMs, but if you
install a binary version of Tktable built for Tcl/Tk 8.4.x, e.g. the one from
ActiveTcl, then you potentially could have conflicts betwee the Tcl/Tk 8.3
and 8.4 shared libraries.
The BWidget package does not require building as there is no C
source code, only Tcl scripts, so it can simply be unzipped in an appropriate
directory using:tar zxvf BWidget-1.7.0.tar.gz. Because it does
not contain any compiled code, it can easily be used on any platform (Windows, Mac, Linux etc.)
without requiring any compiling, although generally it is easier for Windows users
to install ActiveTcl than to obtain BWidget from the sourceforge tcllib site.
To run limmaGUI or affylmGUI on MacOS X, you need to install R 2.1.x from CRAN with X11 Tcl/Tk support. This is not the default! You must click on "custom setup" to enable Tcl/Tk support during R installation.
If library(tcltk) doesn't work, please read the
R for Mac OS X FAQ,
in particular the section
X11 TclTk headers and libraries. If the automatic installation of X11 Tcl/Tk by the
R installer doesn't work for some reason, and you want to install it from source
(as described in the
R for Mac OS X FAQ),
you must have the Apple developer tools installed (which are shipped with all new Macs)
and you must have the X11SDK package installed (which is available on the Xcode CD,
shipped with all new Macs). If you require further information
about this, please contact that R-SIG-MAC mailing list at
https://stat.ethz.ch/mailman/listinfo/r-sig-mac.
Once you have R 2.1.1 installed (with X11 Tcl/Tk) i.e. library(tcltk)
works, then follow the Linux/Unix instructions for installing Tktable and
BWidget, but you may wish to use a pre-built binary X11 version of
Tktable from:
http://bioinf.wehi.edu.au/limmaGUI/Tktable2.8MacOSX_X11.zip
A binary for BWidget is not provided because there is nothing in the package which requires building into a binary format, i.e. it only contains Tcl scripts. See the Linux/Unix section for the URL for BWidget. and instructions on how to unzip it.
Comments/Questions? Contact wettenhall@wehi.edu.au.
Last
modified: 27 June 2005