[BioC] help on analysis ChiP-chip data of affyymetrix Arabidopsistilling array

[Steve Lianoglou]

Hi,

On Jun 26, 2009, at 8:19 AM, Daofeng Li wrote:

> Hi Torsten,
>
> thank you very much for information you provided.
> i am learning~~
>
> Best Wishes.
>
> On Fri, Jun 26, 2009 at 4:45 PM, Torsten Waldminghaus <
> Torsten.Waldminghaus at rr-research.no> wrote:
>
>> I found these papers helpful as starting point:
>>
>> http://www.biomedcentral.com/1471-2105/8/221
>> http://bioinformatics.oxfordjournals.org/cgi/content/full/25/7/954
>> http://www.biomedcentral.com/1471-2105/8/219


In addition to this, you might want to try looking at MAT:
Homepage: http://liulab.dfci.harvard.edu/MAT/
Publication: http://www.ncbi.nlm.nih.gov/pubmed/16895995?dopt=Citation

The original software has been ported from Java and is now maintained  
in Python.

I believe w/ bioconductor 2.4 came an rMAT package, which is an  
implementation of this software in R if you'd like to try it that way:
http://www.bioconductor.org/packages/release/bioc/html/rMAT.html

Hope that helps,
-steve

--
Steve Lianoglou
Graduate Student: Physiology, Biophysics and Systems Biology
Weill Medical College of Cornell University

Contact Info: http://cbio.mskcc.org/~lianos