[BioC] limmaGUI & affylmGUI new features/fixes

[James Wettenhall]

Hi,

Hopefully within a few days, you will see limmaGUI 1.1.0 and 
affylmGUI 1.1.0 on BioC devel.  For now, they are at:
http://bioinf.wehi.edu.au/limmaGUI/
http://bioinf.wehi.edu.au/affylmGUI/

They can be installed with:

install.packages("limmaGUI",contriburl="http://bioinf.wehi.edu.au/limmaGUI")

and

install.packages("affylmGUI",contriburl="http://bioinf.wehi.edu.au/affylmGUI")


New Features/Fixes in both GUIs
--------------------------------
- Recent files now displayed in File menu (only works if you 
    install the limmaGUI/affylmGUI package somwhere where you 
    have write-permission, as the recent files are stored in 
    limmaGUI/etc or affylmGUI/etc.)
- Directory separators are now displayed as back-slashes for
    Windows users, but they are still stored internally as
    forward-slashes.
- Plot titles are now done with title() instead of main= to
    avoid warnings (from using non-standard plotting 
    techniques like tkrplot and HTMLplot.)
- Inconsistent font fixed in entry-box in choose-directory
    dialog.

New Features in limmaGUI
------------------------
- Robust linear model fits now available as an alternative to 
    the usual least-squares linear model fit.
- An "Other" button has been added to the 
    Image-Analysis-File-Format dialog to allow a user to 
    manually enter column-headings for Red/Green Foreground and
    Background intensities for unsupported Image-Analysis file
    formats.

New Features in affylmGUI
-------------------------
- A new worked example with screenshots:  A Malaria Life-Cycle 
    Study from Elizabeth Winzeler's lab at 
    The Scripps Institute
- Fixed a bug in the "Cancel" button of the choose-directory 
    dialog.

More New Features Coming Soon
-----------------------------
- Novice/Advanced modes for the GUIs, so that in Novice mode,
    many of the recommended default options will be chosen
    automatically, rather than asking the user every possible 
    question regarding background-correction method, 
    normalization method, etc.
- Option to choose between tkrplot and the regular R graphics
    device for all plots.
- Updated R-for-windows installation wizards for  
    limmaGUI and affylmGUI
- Any necessary bug fixes

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