[BioC] limmaGUI: target file and spot file

Mark Cowley m.cowley at garvan.org.au
Tue Jul 29 03:19:23 CEST 2008

Hi Jamila,
I noticed that you have not yet received a response.
Generally, if limmaGUI is having a hard time importing your files,  
then limma itself will also have a hard time. I'd recommend that you  
read the limma users guide (type limmaUserGuide() to bring this pdf  
up) and get to a point where you can at least import your data using  
the non-GUI version.
If you then still don't feel comfortable using limma itself, then you  
should be able to proceed again using limmaGUI, but this time with the  
correct targets (and spot types) file.

If you still need help, then please post back to the list with more  
information, particularly the spot types file that you are currently  

Mark Cowley, BSc (Bioinformatics)(Hons)

Peter Wills Bioinformatics Centre
Garvan Institute of Medical Research, Sydney, Australia

On 25/07/2008, at 8:08 PM, Jamila Bernardi wrote:

> Dear all,
> I'm working with the interface limmaGUI using data from two-colors  
> spotted arrays generated by GenePix scanner.
> I have two basic problems regarding  the input data:
> 1) after giving  gal file and target file and after background  
> correction the software doesn't proceed to analysis and it sends  
> this message "limmaGUI was unable to read the image processing files  
> listed in the targets file". I have this problem with recent data,  
> but with previous data the package worked. Why?I have changed  
> nothing in the procedure (analysis of images and exporting txt file).
> 2) the package doesn't read my spot file, I ask some help to prepare  
> correctly this type of input file.
> Thanks to everybody.
> Jam
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