Question: limmaGUI & affylmGUI wizards for Windows & bug fixes
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gravatar for James Wettenhall
15.6 years ago by
James Wettenhall1000 wrote:
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@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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