[BioC] limmaGUI update

[James Wettenhall]

Hi,

I've just uploaded limmaGUI_1.1.2 to :

http://bioinf.wehi.edu.au/limmaGUI/

It has some bug fixes:

- When the user chose not to use background correction, limmaGUI
   gave an error "BCMethod undefined".  Fixed now.
 
- In the color-coded MA plots, the title was being set twice,
   once by the main= argument and once by title().  This is fixed 
   now.  The main argument of plotMA is now set to "" and then
   title() is used.  This is because limmaGUI uses tkrplot which 
   gives warnings when using main=.
 
- Exporting an HTML report failed if used immediately after
   loading in a data set, because the array layout wasn't yet
   defined.  This is fixed now.  The array layout is now 
   defined immediately after reading in the GAL file.
 
- The function plotMAlimmaGUI has been removed from plot.R.
   This was just a temporary function used while experimenting
   with new arguments added to limma's plotMA function.  But
   now that limma has these new arguments, plotMAlimmaGUI is
   no longer needed.  All calls to plotMAlimmaGUI (including
   one in the HTML report function), have now been replaced 
   with calls to plotMA.
 
Regards,
James