[BioC] limmaGUI - venn-diagram & top-table anomaly?
Keith Satterley
keith at wehi.EDU.AU
Wed Sep 9 01:40:44 CEST 2009
Hi Danny,
I've looked into how these functions were coded. They use different
functions to categorize genes, hence the different numbers. The next
version of limmaGUI released with R2.10 in October will use similar
functions. I will email when the developer version is available that
produces matching results for Venn diagrams and toptables. Thanks for
pointing this out,
cheers,
Keith
========================
Keith Satterley
limmaGUI maintainer
=======================
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 0.001 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
>
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