[BioC] limmaGUI & affylmGUI wizards for Windows & bug fixes

James Wettenhall wettenhall at wehi.edu.au
Fri May 28 11:46:28 CEST 2004


Hi,

I've just built Windows installation wizards for limmaGUI 1.0.2
and affylmGUI 1.0.3.  They are designed for Windows users who
don't yet have an R installation (e.g. biologists) and want to
start playing around with microarray analysis using
Graphical User Interfaces (GUIs).

The idea is that the wizard makes you "feel like" you are just
installing R 1.9.0, but as soon as you start RGui.exe, you will
be able to type library(limmaGUI) or library(affylmGUI) without
having to worry about installing any R packages or Tcl/Tk
extensions.

The limmaGUI Windows-installation wizard can be download from:
http://bioinf.wehi.edu.au/limmaGUI/
OR
http://bioinf.wehi.edu.au/limmaGUI/rw1090limmaGUI.exe

The affylmGUI Windows-installation wizard can be download from:
http://bioinf.wehi.edu.au/affylmGUI/
OR
http://bioinf.wehi.edu.au/affylmGUI/rw1090affylmGUI.exe

The limmaGUI wizard includes:
- Everything you would normally get with R 1.9.0 for Windows
- Tktable2.8 and BWidget1.6 Tcl/Tk extensions (built with MinGW)
- statmod_1.0.6, limma_1.6.10, sma_0.5.14, tkrplot_0.0-9,
  R2HTML_1.3, xtable_1.2-3 and limmaGUI_1.0.2

The affylmGUI wizard includes:
- Everything you would normally get with R 1.9.0 for Windows
- Tktable2.8 and BWidget1.6 Tcl/Tk extensions (built with MinGW)
- statmod_1.0.6, limma_1.6.10, Biobase_1.4.14, reposTools_1.4.1,
  affy_1.4.30, affyPLM_1.1.6, gcrma_1.1.0, tkrplot_0.0-9,
  R2HTML_1.3, xtable_1.2-3 and affylmGUI_1.0.3

I don't have time to update these wizards as often as the
limmaGUI and affylmGUI R packages, but if there are any
major problems then of course I can rebuild them.

There are no new features in limmaGUI or affylmGUI since version
1.0.0 (corresponding to the Bioconductor 1.4 Release), BUT THERE
ARE SOME BUG FIXES.

Fixes in both packages:
-----------------------
- "Package Contents" hyperlink added to inst/doc/index.html
- plot.new() call added in limmaGUI() and affylmGUI()
  to ensure that functions like title(...) work when using 
  unconventional plotting methods (tkrplot and HTMLplot).

Fixes in affylmGUI:
-------------------
- Removed get("Myhscale",...) and get("Myvscale",...) from
  ExportHTMLreport function.  They were unnecessary and caused
  errors.
- Fixed the problem of affylmGUI not being able to access
  CDF information if CDF package not available.  For example,
  if you upgrade R, so no longer have a CDF package installed,
  and you load an old affylmGUI data set, it may have assumed
  in 1.0.0 that the CDF package was available, whereas now it
  will download it again if necessary.  This bug appeared in
  the ExportHTMLreport function and also in the showTopTable
  function.
- Updated subscripting of AffyBatch objects to the new method:
  [,i] instead of [i]


Regards,
James

--------------------------------------------------------------------------
James Wettenhall                                  Tel: (+61 3) 9345 2629
Division of Genetics and Bioinformatics           Fax: (+61 3) 9347 0852
The Walter & Eliza Hall Institute         E-mail: wettenhall at wehi.edu.au
 of Medical Research,                     Mobile: (+61 / 0 ) 438 527 921    
1G Royal Parade,
Parkville, Vic 3050, Australia
http://www.wehi.edu.au



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