[BioC] distribution of genes differentially expressed

Johannes Hüsing hannes at ruhrau.de
Wed Apr 9 21:59:01 MEST 2003

Phguardiol at aol.com <Phguardiol at aol.com> [Wed, Apr 09, 2003 at 03:19:00PM CEST]:
> Hi all,
> I d like to know if there is a package in BioC that can identify genes that 
> are differentially expressed between 2 conditions and  analyze their 
> distribution along the chromosomes to say if their distribution is random or 
> if it has a non random distribution with some sort of clusters in some part 
> of the chromosomes... for instance, a tool that could help to detect 
> translocations, loss or gain of chromosomes from the microarray data...

I have worked a bit on it; you can read about it on 
http://www.panix.com/~derwisch/hannes/longrun. There is some code about
the longest run statistic and the scan statistic, which you might find useful
if you dichotomize the differentially expressed genes. As others have pointed
out, this is only one possibility where non-randomness comes in.


Johannes Hüsing   There is something fascinating about science. One gets
hannes at ruhrau.de  such wholesale returns of conjecture from such a 
                  trifling investment of fact.                Mark Twain

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