[R] LimmaGUI

[J.delasHeras at ed.ac.uk]

Quoting solie.alizadeh at utoronto.ca:

> Hi everyone,
>
> I have a question about limmaGUI.I've just started to use the program
> for microarray analysis.My problem is after loading data into Limma
> (with GAl file and RNA targets file),I'm not able to create an M box
> plot and everytime I'm trying to do that, some error appear:
> Error in .find.package(pkg): there is no package called 'tkrplot'
> Error in try(expr,TRUE): could not find function "tkrplot"
> Error in .Tcl.args.objv(...):object "img" not found
> I would also like to know if it's necessary to have a spot type file.
> I'm using R in windows xp,version 2.3.1 and limmaGUI version 1.8.1
> using limma version 2.7.10.
> Could the problem be the version of LimmaGUI I'm using?
> I appreciate your help.

The spots file is not necessary. It is used, however, to define  
individual spots or classes of spots of interests, either to remove  
from normalisation, as control spots, or just to highlight in  
different colours on your plots.

In windows I recommend you install limmaGUI from:

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

go to section 2.3.1, for a binary that will install R 2.1.1 and  
limmaGUI with all dependent packages.

I hope this helps

Jose

PS: remember the BioConductor forum, you're more likely to get useful  
answers about limmaGUI over there.
http://www.bioconductor.org/docs/mailList.html

-- 
Dr. Jose I. de las Heras                      Email: J.delasHeras at ed.ac.uk
The Wellcome Trust Centre for Cell Biology    Phone: +44 (0)131 6513374
Institute for Cell & Molecular Biology        Fax:   +44 (0)131 6507360
Swann Building, Mayfield Road
University of Edinburgh
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UK