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@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.
>  
> 
> Date: Sun, 21 Feb 2010 10:28:07 -0500
> Subject: Re: [BioC] ChIPpeakAnno
> From: julie.zhu@umassmed.edu
> To: genome1976@hotmail.com
> CC: bioconductor@stat.math.ethz.ch
> 
> Hi Som,
> 
> Here is the code to create the RangedData from your input dataframe x assuming
> that the first column of x represents start, the second column of x represents
> end and the third column represents chromosome as either “chr1” or “1” etc.
> 
> myexp = RangedData(IRanges(start = as.numeric(x[,1]), end =
> as.numeric(x[,2])), space=as.character(x[,3]))
> 
> Best regards,
> 
> Julie
> 
> 
> On 2/19/10 6:25 PM, "somnath bandyopadhyay" <genome1976@hotmail.com
> <http://hotmail.com/> > wrote:
> 
>> Hi Julie,
>> Thanks so much for your prompt reply. I have 6000 probesets with
>> corresponding start, end and chromosome information along with strand
>> information in an excel/dataframe format. Could you suggest an easy way to
>> convert it into RangedData?
>>  
>> Thanks,
>> Som.
>>  
>>> > Date: Fri, 19 Feb 2010 09:43:09 -0500
>>> > Subject: Re: [BioC] ChIPpeakAnno
>>> > From: julie.zhu@umassmed.edu <http://umassmed.edu/>
>>> > To: genome1976@hotmail.com <http://hotmail.com/> ;
>>> bioconductor@stat.math.ethz.ch <http://stat.math.ethz.ch/>
>>> > 
>>> > Hi Som,
>>> > 
>>> > myPeakList is RangedData, where "start" is the start (or summit) of the
>>> > binding site, "end" is the end of the binding site, "names" is the name of
>>> > the binding site and "space" is the chromosome name.
>>> > 
>>> > Here is how to create RangedData myexp from a list of binding sites.
>>> > 
>>> > myexp = RangedData(IRanges(start = c(967654, 2010897, 2496704), end =
>>> > c(967754, 2010997, 2496804), names = c("Site1", "Site2", "Site3")), space
=
>>> > c("1", "2", "3"))
>>> > 
>>> > Please see ?annotatePeakInBatch for more examples. Thanks!
>>> > 
>>> > 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 2/19/10 8:52 AM, "somnath bandyopadhyay" <genome1976@hotmail.com
>>> <http://hotmail.com/> > wrote:
>>> > 
>>>> > > 
>>>> > > Could anybody please tell me what the input list (myPeakList) for the
>>>> > > ChIPpeakAnno program look like?
>>>> > > 
>>>> > > I have a list of probeset ids with genomic coordinates coming from a
>>>> nimblegen
>>>> > > 385k chip chip experiment.
>>>> > > 
>>>> > > 
>>>> > > 
>>>> > > Thanks in advance,
>>>> > > 
>>>> > > Som.
>>>> > > 
>>>> > > _________________________________________________________________
>>>> > > Hotmail: Trusted email with Microsoft‚s powerful SPAM protection.
>>>> > > 
>>>> > > [[alternative HTML version deleted]]
>>>> > > 
>>>> > > _______________________________________________
>>>> > > Bioconductor mailing list
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>>>> > > https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>> > > Search the archives:
>>>> > > http://news.gmane.org/gmane.science.biology.informatics.conductor
>>> > 
>>> > 
>>        
>> 
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