R help - Sep 2009 - limmaGUI anomaly: top-table & venn-diagram for linear model

Hello,

In limmaGUI, after running a linear model for a single gene & time point
(mutant vs control), the venn-diagram for differentially expressed genes
with a p-value cut-off gives a different number than the top-table with
the same cut-off (2600 vs. 791).

I have seen the same thing happen before for multiple time points (when
the venn-diagram is more relevant)

Any ideas what is going on?

Thanks

Danny

D.Levin at warwick.ac.uk wrote:
> Hello,
> 
> In limmaGUI, after running a linear model for a single gene & time
point
> (mutant vs control), the venn-diagram for differentially expressed genes
> with a p-value cut-off gives a different number than the top-table with
> the same cut-off (2600 vs. 791).
> 
> I have seen the same thing happen before for multiple time points (when
> the venn-diagram is more relevant)
> 
> Any ideas what is going on?
limmaGUI is a Bioconductor package; ask on the Bioconductor mailing list.

http://bioconductor.org/docs/mailList.html

don't forget to consult packageDescription() and include the maintainer
(who is in the best position to help).

Martin
> 
> Thanks
> 
> Danny
> 
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