Hi Tina,

Limma has some functions related to plotting Venn diagrams, is what you're
looking for?

For example:

> a = runif(100)
> b = runif(100)
> library(limma)
> comparison <- data.frame(de.a=a <= 0.1, de.b=b <= 0.1)
> head(comparison)
   de.a  de.b
1 FALSE  TRUE
2 FALSE  TRUE
3 FALSE FALSE
4 FALSE FALSE
5 FALSE  TRUE
6 FALSE FALSE
> table(comparison)
       de.b
de.a    FALSE TRUE
  FALSE    79   12
  TRUE      9    0
> vc <- vennCounts(comparison)
> vennDiagram(vc)

Also, there are alternative methods at this resource:
http://manuals.bioinformatics.ucr.edu/home/ht-seq

hope this helps,
Vince

On Thu, Mar 1, 2012 at 5:50 PM, Tina Asante Boahene <ma08tta@brunel.ac.uk>wrote:

> Hi all,
>
> I have been analysing some RNA-seq data using the packages DEGseq, edgeR
> and baySeq and I was wondering if anyone could help me to be able
> to produce a plot to show the number of DE found using these packages at
> an FDR of 0.1%. or possibly direct me to any good source that can be used
> to achieve this.
>
> I will certainly appreciate any help.
>
>
> Kind Regards
>
> Tina
> _______________________________________________
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>



-- 
Vince Buffalo
Statistical Programmer
Bioinformatics Core
UC Davis Genome Center
University of California, Davis

"There's real poetry in the real world. Science is the poetry of reality."
-Richard Dawkins

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