affylmGUI          

Introduction


affylmGUI (Affymetrix linear modeling Graphical User Interface) is for Affymetrix data only.
If you have two-color cDNA data, you may wish to try limmaGUI.

affylmGUI Website Links

Main Webpage Contents

  1. Citation for affylmGUI
  2. Software Required by affylmGUI
  3. Installing affylmGUI
    1. Windows Installation Notes
    2. MacOS X Installation Notes
    3. Unix Installation Notes
  4. Running affylmGUI
  5. Trouble Shooting Tcl/Tk and X11
  6. Testing X11 on Mac OS X and Unix
  7. Testing Tcl/Tk
  8. Testing BWidget and Tktable packages
  9. Comments-Questions

1. Citation for affylmGUI

affylmGUI is an implementation of a body of methodological research by the authors and coworkers. Please cite the appropriate methodological papers whenever you use results from the limma software in a publication. Such citations are the main means by which the authors receive professional credit for their work.

Citing limma and affylmGUI in publications will usually involve citing one or more of the methodology papers that the limma software is based on as well as citing the limma software package itself.

If you use limma/affylmGUI for differential expression analysis, please cite reference 1 which describes the linear modeling approach implemented by lmFit and the empirical Bayes statistics implemented by eBayes, topTable etc.

To cite the limma software itself please refer to reference 2 which describes the software package in the context of the Bioconductor project and surveys the range of experimental designs for which the package can be used, including spotspecific dye-effects. The pre-processing capabilities of the package are also described but more briefly, with examples of background correction, spot quality weights and filtering with control spots. This article is also the best current reference for the normexp background correction method.

To cite the GC robust multiarray average (GCRMA) background correction method please cite reference 3.

To cite the robust multiarray average (RMA) background correction method please cite reference 4.

  • 1. Smyth, G. K. (2004). Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments. Statistical Applications in Genetics and Molecular Biology Vol. 3 : Iss. 1, Article 3. (Full text available here.)
  • 2. Smyth, G. K. (2005). Limma: Linear Models for microarray data. In: Bioinformatics and Computational Biology Solutions using R and Bioconductor, R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, W. Huber (eds.), Springer, New York, pages 397-420. (Published 8 August 2005, Publisher web site, PDF)
  • 3. Zhijin Wu1, Rafael A. Irizarry, Robert Gentleman, Francisco Martinez-Murillo, Forrest Spencer. (2004). A Model Based Background Adjustment for Oligonucleotide Expression Arrays In the Journal of the American Statistical Association. Volume 99, Pages 909\226917.
  • 4. Rafael A. Irizarry, Bridget Hobbs, Francois Collin, Yasmin D. Beazer-Barclay, Kristen J. Antonellis, Uwe Scherf, Terence P. Speed. (2003). Exploration, normalization, and summaries of high density oligonucleotide array probe level data In the Journal Biostatistics. Volume 4(2), Pages 249\226264.

2. Software required by affylmGUI.

affylmGUI uses the R package named "tcltk". This is installed with all standard installations of R.
affylmGUI is dependent on the limma, affy, BiocInstaller, affyio, tkrplot, affyPLM, R2HTML, xtable, gcrma and AnnotationDbi R packages and their dependencies.
The biocLite installation process described above will automatically install all these R packages.

affylmGUI uses Tcl/Tk. It is a programming language separate from R and needs to be on each platform.
affylmGUI uses two packages written in the Tcl/Tk language, namely, BWidget and Tktable, that need to be present also.
affylmGUI uses the X11 windowing system on Mac OS X and on Unix platforms.
affylmGUI uses the built in windowing system on the Microsoft Windows platform.

3. Installing affylmGUI

affylmGUI is distributed as open-source software under the LGPL license. If not already done, install the current version of R from CRAN, the Comprehensive R Archive Network
Install Bioconductor as described on the Bioconductor web site
Install the affylmGUI package similar to the Install Package instructions on the Bioconductor web site
In brief this is:

source("http://bioconductor.org/biocLite.R")
biocLite("affylmGUI",lib=.Library)
This will install affylmGUI and other R packages that affylmGUI depends on, if they are not already installed.

(a).Microsoft Windows Installation.

The standard R install includes the R tcltk package.
The Tcl/Tk language tools are installed in C:\R\R-3.x.y\Tcl, if R is installed in C:\R\R-3.x.y.
The two Tcl/Tk packages, BWidget and Tktable.are installed in C:\R\R-3.x.y\Tcl\lib.
No further installations are necessary.

(b).Mac OS X Installation.

The standard R install includes the R tcltk package.
The Tcl/Tk language tools are installed in /usr/local/lib,/usr/local/include and /usr/local/bin.
The two Tcl/Tk packages, BWidget and Tktable are installed in /usr/local/lib/tcl8.6.
X11 is needed on Mac OS X. To save duplicating instructions, please refer to the installation notes for the Rcmdr package, which uses X11 in a similar manner to that required by affylmGUI. The notes on how to install X11 for the Mac are located in the "Mac OS X" section in the R Commander Installation Notes. If you encounter problems refer to the "Mac OS X Trouble-shooting" section in the Rcmdr url mentioned above. If BWidget and/or Tktable are not found, consult the trouble shooting section below.

(c).Unix Installation.

The standard R install includes the R tcltk package.
It does not include the Tcl/Tk language tools.
It does not include the two Tcl/Tk packages, BWidget and Tktable.
The Tcl/Tk language is normally already installed on Unix platforms. If it is not consult the trouble shooting section below.
If BWidget and/or Tktable are not found, consult the trouble shooting section below.

3. Running affylmGUI

Start up R (or RGui), load the affylmGUI package with

library(affylmGUI)
							
To run affylmGUI, at the R prompt type:
affylmGUI()
							
and press Enter.

On MS Windows, the affylmGUI package works best with the single-document Rgui interface (SDI).
Under the default multiple-document interface (MDI), Tk dialog boxes may not stay on top of the main R window. This is a general issue with applications, such as the affylmGUI and RCmdr, that are based on the tcltk package.

4. Trouble shooting.Tcl/Tk and X11 problems.

Requirements of R.

First step is to establish whether R has the capability to use Tcl/Tk and X11. To do this issue the capabilities() command at the R prompt.
The output of this function indicates a TRUE or FALSE value for various abilities.

MS Windows
On MS Windows you need a TRUE value for tcltk. The value for X11 is irrelevant for MS Windows.

Mac OS X:
On Mac OS X you need a TRUE value for Tcl/Tk and also for X11.
If either value is FALSE consult the R Commander Installation Notes, in particular read the notes under the "Mac OS X" heading.

Unix
On Unix you need a TRUE value for Tcl/Tk and also for X11.
If R has been compiled locally, it may not have been compiled with the " --with-x --with-tcltk " switches.
Examine the config.log file to check the switches used when it was compiled. Recompile and reinstall if necessary.
Tcl/Tk is usually installed with a standard Unix installation. If not consult your sytem administrator. X11 is usually installed with a standard Unix installation. If not consult your sytem administrator.

Testing X11 on Mac OS X and Unix.

Before running R, Test X11 by running a common X application like "xclock". For example:
xclock
If you do not get a clock showing on your chosen display then your X11 setup needs to be addressed.
Here are some pointers to check on the various platforms.

On MS Windows
test not applicable.

On Mac OS X:
On my Mac, xclock is located in /usr/X11/bin. If necessary, use the locate command to find the xclock file.
You may need to start the X11 application on your Mac, although on my Mac, X11 automatically starts when xclock is run.

On Unix:
On my Linux machine, xclock is located in /usr/bin. If necessary, use the locate command to find the xclock file.
If you receive a response like:
X connection to localhost:11.0 broken (explicit kill or server shutdown)
You may need the DISPLAY environment variable set. For example:
export DISPLAY=yourpc.domain.com.au:0.0
If, after running xclock again you now get a message like:
Error: Can not open display: yourpc.domain.com.au:0.0
You need to start an Xserver on the computer you are hoping to see the display on.
This could be the X11 application on your Unix workstation or Mac. On MS Windows it could be XWin32 or similar.

Testing Tcl/Tk.

At an R prompt, load the tcltk package.
>library(tcltk) If there is no error message then the Tcl/Tk language has been found on your system.
If there is an error message, for example:

On MS Windows:
error: Tcl/Tk support files were not installed
Re install R for MS Windows as it includes the Tcl/Tk language.

On Mac OS X:
error: Tcl/Tk support files were not installed
Re install R for Mac OS X as it includes the Tcl/Tk language.
Note that the Aqua-compatible (but X11-incompatible) Tcl/Tk directories
will generally be in /Library/Tcl/. affylmGUI cannot use these.

On Unix:
Error message re location of tcl libraries.
You will need to install Tcl/Tk on your unix machine.
You may need system manager privileges to do this.

Testing BWidget and Tktable packages.

When R loads the tcltk package it sets a path that it will look in for Tcl/Tk packages.
This path is called "auto_path". to see it's value use the following command:
tclvalue("auto_path")

On MS Windows:
A typical output is:
[1] "C:/R/R-3.0.2/Tcl/lib64 C:/R/R-3.0.2/Tcl/lib/tcl8.5 C:/R/R-3.0.2/Tcl/lib C:/R/R-3.0.2/bin/lib C:/R/R-3.0.2/Tcl/lib/tk8.5 C:/R/R-3.0.2/Tcl/lib/tk8.5/ttk C:/R/R-3.0.2/library/tcltk/exec"

On Mac OS X:
A typical output is:
[1] "/usr/local/lib/tcl8.6 /usr/local/lib ./lib /usr/local/lib/tk8.6 /usr/local/lib/tk8.6/ttk /Library/Frameworks/R.framework/Resources/library/tcltk/exec"

On Unix:
A typical output is:
[1] "/usr/share/tcl8.4 /usr/share /usr/lib64 /usr/share/tk8.4 /usr/local/bioinfsoftware/R/R-3.0.2/lib64/R/library/tcltk/exec"

If you wish to add further paths to be searched for tcl/tk packages, use the command: addTclPath("/Users/keith/lib"), for example.

To install Bwidget download it from http://sourceforge.net/projects/tcllib/ Click the Download button (current version is bwidget-1.9.7.zip), unzip it (Example command is "unzip bwidget-1.9.7.zip") into /usr/lib or another location on the auto_path. The BWidget package is written entirely in the tcl language and hence only needs to be placed in an auto_path location.
To install Tktable download from http://tktable.sourceforget.net. From this site, select "File Distributions, select the "tktable" link, select the latest version (currently 2.10), then select the tar.gz file (currently "Tktable2.10.tar.gz"). Save it to a suitable location, unzip and untar it (Example command is "tar zxf Tktable2.10.tar.gz"). look in the Tktable directory and read the README.txt file installation instructions. If you installed Tktable into a location in your home directory you would put that location into the auto_path value, as explained above. The Tktable package includes C code and needs compiling and installing.
If the directories, Tktable2.10 and bwidget-1.9.7 were both located in the directory "TkExtensions" in your home directory, then auto_path need only to contain "your_home_directory/TkExtensions" to allow tcltk functions to find the Tktable and Bwidget packages.

5. Comments/Questions

Any comments or questions. Please contact Keith Satterley at The Walter & Eliza Hall Institute of Medical Research..

Last modified: 29-11-2013