segmentation for Affy SNP arrays
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Yu Chuan Tai ▴ 440
@yu-chuan-tai-1534
Last seen 8.2 years ago
Hi List, Just want to know if there is any software which does segmentation on copy number estimates from Affy SNP arrays? It looks like GLAD, DNAcopy and snapCGH are only for array CGH...... Thanks! Yu Chuan
SNP CGH affy GLAD snapCGH SNP CGH affy GLAD snapCGH • 1.3k views
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@kasper-daniel-hansen-2979
Last seen 9 weeks ago
United States
You can check out aroma.affymetrix from www.braju.com/R Kasper On Sep 18, 2007, at 12:51 PM, Yu Chuan Tai wrote: > Hi List, > > Just want to know if there is any software which does segmentation > on copy number estimates from Affy SNP arrays? It looks like GLAD, > DNAcopy > and snapCGH are only for array CGH...... > > Thanks! > Yu Chuan > > _______________________________________________ > 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
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Thanks! Looks like aroma.affymetrix uses GLAD model for segmentation...... Is there any other software available? Yu Chuan On Tue, 18 Sep 2007, Kasper Daniel Hansen wrote: > You can check out aroma.affymetrix from www.braju.com/R > > Kasper > > On Sep 18, 2007, at 12:51 PM, Yu Chuan Tai wrote: > >> Hi List, >> >> Just want to know if there is any software which does segmentation >> on copy number estimates from Affy SNP arrays? It looks like GLAD, DNAcopy >> and snapCGH are only for array CGH...... >> >> Thanks! >> Yu Chuan >> >> _______________________________________________ >> 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
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Dear Yu, The packages that you mention (and some others, too) can be used with Affy SNP arrays. The paper by Yu et al., 2007, BMC Bioinformatics,8: 145+ (http://www.biomedcentral.com/1471-2105/8/145/abstract), for example, compares their performance. (Please note that we have some problems with the way our RJaCGH package was used and we are working on a reply. I can send further details off-list). Best, R. On Tuesday 18 September 2007 22:38, Yu Chuan Tai wrote: > Thanks! Looks like aroma.affymetrix uses GLAD model for segmentation...... > Is there any other software available? > > Yu Chuan > > On Tue, 18 Sep 2007, Kasper Daniel Hansen wrote: > > You can check out aroma.affymetrix from www.braju.com/R > > > > Kasper > > > > On Sep 18, 2007, at 12:51 PM, Yu Chuan Tai wrote: > >> Hi List, > >> > >> Just want to know if there is any software which does segmentation > >> on copy number estimates from Affy SNP arrays? It looks like GLAD, > >> DNAcopy and snapCGH are only for array CGH...... > >> > >> Thanks! > >> Yu Chuan > >> > >> _______________________________________________ > >> 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 > > _______________________________________________ > 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 -- Ram?n D?az-Uriarte Statistical Computing Team Centro Nacional de Investigaciones Oncol?gicas (CNIO) (Spanish National Cancer Center) Melchor Fern?ndez Almagro, 3 28029 Madrid (Spain) Fax: +-34-91-224-6972 Phone: +-34-91-224-6900 http://ligarto.org/rdiaz PGP KeyID: 0xE89B3462 (http://ligarto.org/rdiaz/0xE89B3462.asc) **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en s...{{dropped}}
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Hi Ramon, Thanks for your info. I will look at the paper you mentioned below and get back to you if I need more details about your package. Best, Yu Chuan On Wed, 19 Sep 2007, Ramon Diaz-Uriarte wrote: > Dear Yu, > > > The packages that you mention (and some others, too) can be used with Affy SNP > arrays. The paper by Yu et al., 2007, BMC Bioinformatics,8: 145+ > (http://www.biomedcentral.com/1471-2105/8/145/abstract), for example, > compares their performance. (Please note that we have some problems with the > way our RJaCGH package was used and we are working on a reply. I can send > further details off-list). > > Best, > > R. > > > On Tuesday 18 September 2007 22:38, Yu Chuan Tai wrote: >> Thanks! Looks like aroma.affymetrix uses GLAD model for segmentation...... >> Is there any other software available? >> >> Yu Chuan >> >> On Tue, 18 Sep 2007, Kasper Daniel Hansen wrote: >>> You can check out aroma.affymetrix from www.braju.com/R >>> >>> Kasper >>> >>> On Sep 18, 2007, at 12:51 PM, Yu Chuan Tai wrote: >>>> Hi List, >>>> >>>> Just want to know if there is any software which does segmentation >>>> on copy number estimates from Affy SNP arrays? It looks like GLAD, >>>> DNAcopy and snapCGH are only for array CGH...... >>>> >>>> Thanks! >>>> Yu Chuan >>>> >>>> _______________________________________________ >>>> 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 >> >> _______________________________________________ >> 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 > > -- > Ram?n D?az-Uriarte > Statistical Computing Team > Centro Nacional de Investigaciones Oncol?gicas (CNIO) > (Spanish National Cancer Center) > Melchor Fern?ndez Almagro, 3 > 28029 Madrid (Spain) > Fax: +-34-91-224-6972 > Phone: +-34-91-224-6900 > > http://ligarto.org/rdiaz > PGP KeyID: 0xE89B3462 > (http://ligarto.org/rdiaz/0xE89B3462.asc) > > > > **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. > **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. > >
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Hi Yu, You might also have a look at Dchip, CNAG and GEMCA. Theye are no R packages but should be able to calculate the CNs for you up to the 500k chips. However I would like to join Yu here in one point: Is there already any package which can handle the new SNP6.0 chips? As far as I know not yet, or is there one? Regards, Benjamin -----Urspr?ngliche Nachricht----- Von: bioconductor-bounces at stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] Im Auftrag von Ramon Diaz-Uriarte Gesendet: Wednesday, September 19, 2007 11:10 AM An: bioconductor at stat.math.ethz.ch Betreff: Re: [BioC] segmentation for Affy SNP arrays Dear Yu, The packages that you mention (and some others, too) can be used with Affy SNP arrays. The paper by Yu et al., 2007, BMC Bioinformatics,8: 145+ (http://www.biomedcentral.com/1471-2105/8/145/abstract), for example, compares their performance. (Please note that we have some problems with the way our RJaCGH package was used and we are working on a reply. I can send further details off-list). Best, R. On Tuesday 18 September 2007 22:38, Yu Chuan Tai wrote: > Thanks! Looks like aroma.affymetrix uses GLAD model for segmentation...... > Is there any other software available? > > Yu Chuan > > On Tue, 18 Sep 2007, Kasper Daniel Hansen wrote: > > You can check out aroma.affymetrix from www.braju.com/R > > > > Kasper > > > > On Sep 18, 2007, at 12:51 PM, Yu Chuan Tai wrote: > >> Hi List, > >> > >> Just want to know if there is any software which does segmentation > >> on copy number estimates from Affy SNP arrays? It looks like GLAD, > >> DNAcopy and snapCGH are only for array CGH...... > >> > >> Thanks! > >> Yu Chuan > >> > >> _______________________________________________ > >> 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 > > _______________________________________________ > 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 -- Ram?n D?az-Uriarte Statistical Computing Team Centro Nacional de Investigaciones Oncol?gicas (CNIO) (Spanish National Cancer Center) Melchor Fern?ndez Almagro, 3 28029 Madrid (Spain) Fax: +-34-91-224-6972 Phone: +-34-91-224-6900 http://ligarto.org/rdiaz PGP KeyID: 0xE89B3462 (http://ligarto.org/rdiaz/0xE89B3462.asc) **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en s...{{dropped}} _______________________________________________ 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 -- Pflichtangaben gem?? Gesetz ?ber elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG): Universit?tsklinikum Hamburg-Eppendorf K?rperschaft des ?ffentlichen Rechts Gerichtsstand: Hamburg Vorstandsmitglieder: Prof. Dr. J?rg F. Debatin (Vorsitzender) Dr. Alexander Kirstein Ricarda Klein Prof. Dr. Dr. Uwe Koch-Gromus
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@sylviamerkukmuensterde-1608
Last seen 8.2 years ago
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Rob Scharpf ▴ 250
@rob-scharpf-1931
Last seen 8.2 years ago
> Message: 1 > Date: Wed, 19 Sep 2007 15:26:18 +0200 > From: "Benjamin Otto" <b.otto at="" uke.uni-hamburg.de=""> > Subject: Re: [BioC] segmentation for Affy SNP arrays > To: "'Ramon Diaz-Uriarte'" <rdiaz at="" cnio.es="">, > <bioconductor at="" stat.math.ethz.ch=""> > Message-ID: <001501c7fac0$b0e0b610$9f05a20a at matrix.com> > Content-Type: text/plain; charset="utf-8" > > Hi Yu, > > You might also have a look at Dchip, CNAG and GEMCA. Theye are no R > packages > but should be able to calculate the CNs for you up to the 500k chips. Once you have SNP-level summaries of genotype and/or copy number, the R package VanillaICE can be used to fit a hidden Markov model. The underlying states (e.g., deletion, amplification, etc) are determined by whether genotype, copy number, or both are available (the available SNP-level summaries define the class of the object). We've only tested on the Affymetrix 100k, 500k and Illumina platforms. But as long as you have the physical position of a SNP and a corresponding estimate of copy number and/or genotype, the 'Vanilla' HMM should be platform-independent. Rob > -----Urspr?ngliche Nachricht----- > Von: bioconductor-bounces at stat.math.ethz.ch > [mailto:bioconductor-bounces at stat.math.ethz.ch] Im Auftrag von Ramon > Diaz-Uriarte > Gesendet: Wednesday, September 19, 2007 11:10 AM > An: bioconductor at stat.math.ethz.ch > Betreff: Re: [BioC] segmentation for Affy SNP arrays > > Dear Yu, > > > The packages that you mention (and some others, too) can be used > with Affy > SNP arrays. The paper by Yu et al., 2007, BMC Bioinformatics,8: 145+ > (http://www.biomedcentral.com/1471-2105/8/145/abstract), for example, > compares their performance. (Please note that we have some problems > with the > way our RJaCGH package was used and we are working on a reply. I > can send > further details off-list). > > Best, > > R. >
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