[BioC] Detecting overrepresented genomic loci

Robert Gentleman rgentlem at fhcrc.org
Wed Mar 30 00:04:54 CEST 2005

It depends on what you mean by that. Two relatively easy things to do,  
are to look at chromosomes (possibly 1/2 of chromosomes) this  
information is kept in the xxxCHR environment for each data package.  
The other relatively easy calculation is to use xxxMAP files, which  
group probes by cytochrome band.

These would then let you construct two way tables, one direction is  
expressed/not (if that is really the way you want to do things - let me  
suggest a Bayesian approach - EBarrays or limma) and the other  
direction in the table is the category (either chromosome or cytochrome  
band). You could then use virtually any two way table test (but do be  
careful with Fisher's exact test, as you may end up with a very large  
and hence long running computation).

Doing something more (like looking for amplicons) is a bit harder - but  

best wishes

On Mar 29, 2005, at 1:07 PM, jeffrey rasmussen wrote:

> Hi all,
> My goal is to discover regions with multiple adjacent genes  
> coordinately regulated. Are there any packages that would allow one to  
> test for genomic loci that are overrepresented in a subset of genes  
> versus the remaining genes on the chip? I have tried using the  
> geneplotter package to visualize the genomic distribution of  
> differentially expressed genes, however, I have found it difficult to  
> identify candidate loci from these plots because neighboring genes are  
> indistinguishable from each other on the output graphic.
> Thanks,
> Jeff.
> __________________________________
> Jeffrey Rasmussen
> Research Consultant, Bioinformatics
> Department of Immunology
> University of Washington
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| Robert Gentleman              phone: (206) 667-7700                    
| Head, Program in Computational Biology   fax:  (206) 667-1319   |
| Division of Public Health Sciences       office: M2-B865               
| Fred Hutchinson Cancer Research Center                                 
| email: rgentlem at fhcrc.org                                              

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