[BioC] hyperG over chromosome position...?

[Dario Greco]

hi,
actually i want just to check if the genes that change in a  
microarray experiment are located in "clusters" on the chromatin.
the question is: if there are 10 genes annotated in a given  
chromosomal region and i find 7 of them as up-regulated (let me be  
optimistic), then it could eventually mean something...
thanks again
d

-- 

Dario Greco

Institute of Biotechnology - University of Helsinki
Building Cultivator II
P.O.Box 56    Viikinkaari 4
FIN-00014    Finland

Office: +358 9 191 58951
Fax: +358 9 191 58952
Mobile: +358 44 023 5780

Lab WebPage:
http://www.biocenter.helsinki.fi/bi/dna-microarray/

Personal WebPage:
http://www.biocenter.helsinki.fi/bi/dna-microarray/dario.htm



On Jan 11, 2007, at 10:02 PM, James W. MacDonald wrote:

> Dario Greco wrote:
>> hi all,
>> i would like to perform hyperGTest using the chromosome position   
>> (stored usually in pkgMAP environment).
>> how could it be possible?
>> thank you for your help!
>> greetings
>> d
> Is the goal to find chromosomal regions that have higher than  
> expected expression? If so, I don't think you want a HyperGeometric  
> test. Instead you probably want something like the reb package.  
> There might be one or two other packages designed for this sort of  
> thing, but I can't remember offhand what they are.
>
> You might look through the biocViews pages:
>
> http://www.bioconductor.org/packages/1.9/BiocViews.html
>
> Best,
>
> Jim
>
>
>
> -- 
> James W. MacDonald, M.S.
> Biostatistician
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
> 734-647-5623
>
>
> **********************************************************
> Electronic Mail is not secure, may not be read every day, and  
> should not be used for urgent or sensitive issues.