[BioC] affylmGUI gene list from Venn diagram, was: (no subject)

[James Wettenhall]

Hi Simon,

No sorry, there is no way at the moment to get a list of genes 
from the venn diagram in affylmGUI, but depending on how 
"CLI challenged" you are, you could ask on this mailing list 
about doing this using the limma functions classifyTestsF and 
vennCounts and combining this information with your list of 
probe set IDs from the CDF package or gene names from the 
annotation package.  

It is certainly possible to extract this information (at the 
command-line) from affylmGUI data objects, but I don't have time
to try this out right now, so if you ask on the mailing 
list about how to do it at the command-line with limma and 
affy, then I can easily explain how to translate the solution 
for use with affylmGUI.  You might want to look at the 
extract.pdf vignette in affylmGUI.

Regards,
James

 On Wed, 16 Jun 2004, Simon Kidd wrote:

> Hi,
> 
> We are CLI challenged so we have been using affylmgui for our 
> analysis. Our analysis has been to make three comparisons and then to 
> look at the genes which are in common between the three. Affylmgui 
> allows one to visually see the result of the comparison with a Venn 
> diagram, we would like to get a list of the genes (and appropriate 
> statistics) in the various intersections. Is there a way of doing 
> this?
> 
> thanks,
> 
> Simon
> 
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> 

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