[BioC] ChIPpeakAnno

[Joern Toedling]

Hi Som,

regarding the analysis of ChIP-chip data from Nimblegen arrays, you can also
have a look at the package Ringo, the data package ccTutorial and their
vignettes. I would recommend to remap the probe sequences from the NDF to the
current assembly of the mouse genome (mm9) using alignment tools like
Exonerate or functions of Biostrings, and to retrieve the current gene
annotation from databases, e.g. using biomaRt. 

Regards,
Joern


On Thu, 25 Feb 2010 19:35:13 -0500, Julie Zhu wrote
> Dear Som,
> 
> I think you could use pdInfoBuilder
> 
> (http://www.bioconductor.org/packages/bioc/vignettes/pdInfoBuilder/inst/doc/
> BuildingPDInfoPkgs.pdf) to build an annotation package to store all the
> probe information including gene symbol, gene id etc from the ndf 
> and pos file. Building annotation dataset is beyond ChIPpeakAnno 
> though.  I am ccing the Bioc list to get experts’ pointers on 
> building annotation packages.
> 
> Best regards,
> 
> Julie
> 
> *******************************************
> Lihua Julie Zhu, Ph.D
> Research Associate Professor
> Program Gene Function and Expression
> University of Massachusetts Medical School
> 364 Plantation Street, Room 613
> Worcester, MA 01605
> 508-856-5256
> http://www.umassmed.edu/pgfe/faculty/zhu.cfm
> 
> On 2/25/10 4:40 PM, "somnath bandyopadhyay" <genome1976 at hotmail.com> 
> wrote:
> 
> > Dear Julie,
> >  
> > Thanks so much for the pointers and all the help. It worked! I needed your
> > help with one more thing and was wondering if using ChIPpeakAnno would be the
> > ideal thing to do.
> >  
> > I have been analyzing Nimblegen 385k chip-chip data of mm8 refseq genome. I
> > have the .ndf and .pos files for the chip. What would be best way to build an
> > annotation file for the entire chip so that at the end of the day I have a
> > gene symbol, gene id etc. for each single probeset (~385,000) on the chip?
> >  
> > Thanks a lot in advance!
> > Best Regards,
> > Som.
> >  
> > 


---
Joern Toedling
Institut Curie -- U900
26 rue d'Ulm, 75005 Paris, FRANCE
Tel. +33 (0)156246927