Dear Som,
I think you could use pdInfoBuilder
(
http://www.bioconductor.org/packages/bioc/vignettes/pdInfoBuilder/ins
t/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 expertsâ 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 âchr1â
or â1â 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 Microsoftâs powerful SPAM
protection.
>>>> > >
>>>> > > [[alternative HTML version deleted]]
>>>> > >
>>>> > > _______________________________________________
>>>> > > Bioconductor mailing list
>>>> > > Bioconductor@stat.math.ethz.ch <http: stat.math.ethz.ch=""/>
>>>> > >
https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>> > > Search the archives:
>>>> > >
http://news.gmane.org/gmane.science.biology.informatics.conductor
>>> >
>>> >
>>
>>
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