help on analysis ChiP-chip data of affyymetrix Arabidopsis tilling array

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lidaof ▴ 450

@lidaof-1917

Last seen 10.0 years ago

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Dear list members, i am totally new to this area can anyone recommend some material for me to study? Thanks in advance. Best Regards. -- Daofeng Li,PhD Candidate China Agricultural University [[alternative HTML version deleted]]

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ADD COMMENT • link updated 15.5 years ago by Torsten Waldminghaus ▴ 80 • written 15.5 years ago by lidaof ▴ 450

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Torsten Waldminghaus ▴ 80

@torsten-waldminghaus-3502

Last seen 10.3 years ago

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 However, I use the limma package from R to get the data in shape (background subtraction, normalization). Than I make a gff file out of the data and use CoCAS to detect the peaks. This might not be the best way (any better suggestions are welcome) since I'm as well a beginner rather than an expert. Good luck, Torsten -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Daofeng Li Sent: 26. juni 2009 10:33 To: bioconductor at stat.math.ethz.ch Subject: [BioC] help on analysis ChiP-chip data of affyymetrix Arabidopsistilling array Dear list members, i am totally new to this area can anyone recommend some material for me to study? Thanks in advance. Best Regards. -- Daofeng Li,PhD Candidate China Agricultural University [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

ADD COMMENT • link 15.5 years ago Torsten Waldminghaus ▴ 80

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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@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 > > However, I use the limma package from R to get the data in shape > (background subtraction, normalization). Than I make a gff file out of > the data and use CoCAS to detect the peaks. This might not be the best > way (any better suggestions are welcome) since I'm as well a beginner > rather than an expert. > > Good luck, > > Torsten > > -----Original Message----- > From: bioconductor-bounces@stat.math.ethz.ch > [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of Daofeng Li > Sent: 26. juni 2009 10:33 > To: bioconductor@stat.math.ethz.ch > Subject: [BioC] help on analysis ChiP-chip data of affyymetrix > Arabidopsistilling array > > Dear list members, > > i am totally new to this area > can anyone recommend some material for me to study? > Thanks in advance. > > Best Regards. > > -- > Daofeng Li,PhD Candidate > China Agricultural University > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Daofeng Li,PhD Candidate China Agricultural University [[alternative HTML version deleted]]

ADD REPLY • link 15.5 years ago lidaof ▴ 450

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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

ADD REPLY • link 15.5 years ago Steve Lianoglou ★ 13k

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Hi steve, Thank you for information~~ i had read some material mentioned above is there any package specillaly desighed to analysis ChIP along with tilling array of Affymetrix company? Best Regards. On Fri, Jun 26, 2009 at 9:03 PM, Steve Lianoglou < mailinglist.honeypot@gmail.com> wrote: > 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@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 > > > > -- Daofeng Li,PhD Candidate China Agricultural University [[alternative HTML version deleted]]

ADD REPLY • link 15.5 years ago lidaof ▴ 450

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Sorry, i found MAT might used for Affymetrix arrays~~~ Best. On Fri, Jun 26, 2009 at 9:44 PM, Daofeng Li <lidaof@gmail.com> wrote: > Hi steve, > Thank you for information~~ > i had read some material mentioned above > is there any package specillaly desighed to analysis ChIP along > with tilling array of Affymetrix company? > > Best Regards. > On Fri, Jun 26, 2009 at 9:03 PM, Steve Lianoglou < > mailinglist.honeypot@gmail.com> wrote: > >> 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@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 >> >> >> >> > > > -- > Daofeng Li,PhD Candidate > China Agricultural University > -- Daofeng Li,PhD Candidate China Agricultural University [[alternative HTML version deleted]]

ADD REPLY • link 15.5 years ago lidaof ▴ 450

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