[R] limmaGUI anomaly: top-table & venn-diagram for linear model

[D.Levin at warwick.ac.uk]

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