[BioC] Overlapping genes in subsets of lists

[Heike Pospisil]

Hi Thomas,

I guess, the latter approach will work. I am going to test this.

Thanks to you (and Sean who suggested a similar approach),
Heike

On Wednesday 08 October 2008 15:23, Thomas Hampton wrote:
> I would use the table function in R, which will tell you how many
> times gene X appears. If you have 100 lists, the maximum frequency
> is 100, as long as you make each gene unique on any given list.
>
> Then you can sort by frequency to see which genes come up most often.
>
> Another approach I have used is to hierarchically cluster the the lists,
> which will tell you which gene lists have the most genes in common.
>
> Hope this helps,
>
> Tom
>
> On Oct 8, 2008, at 8:34 AM, Heike Pospisil wrote:
> > Hello there,
> >
> > I have 100 lists of differentially expressed genes, and I am trying
> > to find
> > genes overrepresented in these 100 lists (I call them a 'cluster of
> > genes').
> > What's worse, I expect not only one cluster of genes, but three or
> > four or
> > five of them. That is why, a simple intersection() will not help. I
> > wish to
> > had a function that can select all genes which appear in 100% of 33
> > lists of
> > genes (cluster 1), all genes which appear in 100% of 22 lists
> > (cluster 2) and
> > all genes which appear in 100% of the remaining 45 lists (cluster
> > 3). (I hope
> > my explanation is clear).
> >
> > Does anybody know a package or a strategy how to define such clusters?
> >
> > Thanks and best,
> > Heike
> > --
> > Dr. Heike Pospisil      | pospisil at zbh.uni-hamburg.de
> > University of Hamburg   | Center for Bioinformatics
> > Bundesstrasse 43        | 20146 Hamburg, Germany
> > phone:+49-40-42838-7303 | fax: +49-40-42838-7312
> >
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-- 
Dr. Heike Pospisil      | pospisil at zbh.uni-hamburg.de
University of Hamburg   | Center for Bioinformatics 
Bundesstrasse 43        | 20146 Hamburg, Germany 
phone:+49-40-42838-7303 | fax: +49-40-42838-7312