To participate in the IBC2004 Microarray Workshop, you are expected to have installed R 1.9.1 on your computer beforehand.
This webpage gives a list of the R packages required for the IBC2004 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 Windows installation wizard below will appear identical to the 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 IBC2004 included. The R packages are listed in the next session.
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 IBC2004 R for Windows Installation Wizard described in Section 3 which should include Tktable and BWidget.
In Linux/Unix, it may be a little more difficult (than in Windows) to tell R where to find the Tcl/Tk extensions you have installed. 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 in the R-Tcl/Tk search path, type:
library(tcltk)
tclRequire("Tktable")
tclRequire("BWidget")
For Linux/Unix operating systems, you can download the source of the 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 Tktable2.8.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.
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
To run limmaGUI or affylmGUI on MacOS X, you need to be running R-Tcl/Tk in X11 (not Aqua). This is the default for R 1.9.1 for MacOS X installed from CRAN. 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 1.9.1 installed (with X11 Tcl/Tk), then read 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:
3 July 2004