Bioconductor Digest, Vol 84, Issue 19
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Dick Beyer ★ 1.4k
@dick-beyer-26
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I was wondering if anyone is working on OMICS integration? Specifically, integrating data from gene expression, proteomics, and metabolomics for the same samples. I know about integrOmics: KL Cao, I Gonz?lez, S D?jean, integrOmics: an R package to unravel relationships between two omics datasets, BIOINFORMATICS APPLICATIONS NOTE Vol. 25 no. 21 2009, pages 2855?2856 but that package is not yet available. Thanks very much, Dick ********************************************************************** ********* Richard P. Beyer, Ph.D. University of Washington Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 Seattle, WA 98105-6099 http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html http://staff.washington.edu/~dbeyer ********************************************************************** *********
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@martin-morgan-1513
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On 02/19/2010 11:51 AM, Dick Beyer wrote: > I was wondering if anyone is working on OMICS integration? > Specifically, integrating data from gene expression, proteomics, and > metabolomics for the same samples. > > I know about integrOmics: > > KL Cao, I Gonz?lez, S D?jean, integrOmics: an R package to unravel > relationships between two omics datasets, BIOINFORMATICS APPLICATIONS > NOTE Vol. 25 no. 21 2009, pages 2855?2856 > > but that package is not yet available. Speaking a little out of my comfort zone, but http://cran.r-project.org/web/packages/PMA/index.html as a statistical methodology seems well motivated. Martin > > Thanks very much, > Dick > ******************************************************************** *********** > > Richard P. Beyer, Ph.D. University of Washington > Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 > Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 > Seattle, WA 98105-6099 > http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html > http://staff.washington.edu/~dbeyer > ******************************************************************** *********** > > > > > _______________________________________________ > 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 -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
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Hi Martin, Thanks for the excellent pointer to PMA. (Sorry about the poor choice of subject lines. Very nice of you to respond!) Thanks very much, Dick ********************************************************************** ********* Richard P. Beyer, Ph.D. University of Washington Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 Seattle, WA 98105-6099 http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html http://staff.washington.edu/~dbeyer ********************************************************************** ********* On Sat, 20 Feb 2010, Martin Morgan wrote: > On 02/19/2010 11:51 AM, Dick Beyer wrote: >> I was wondering if anyone is working on OMICS integration? >> Specifically, integrating data from gene expression, proteomics, and >> metabolomics for the same samples. >> >> I know about integrOmics: >> >> KL Cao, I Gonz?lez, S D?jean, integrOmics: an R package to unravel >> relationships between two omics datasets, BIOINFORMATICS APPLICATIONS >> NOTE Vol. 25 no. 21 2009, pages 2855?2856 >> >> but that package is not yet available. > > Speaking a little out of my comfort zone, but > > http://cran.r-project.org/web/packages/PMA/index.html > > as a statistical methodology seems well motivated. > > Martin > >> >> Thanks very much, >> Dick >> ******************************************************************* ************ >> >> Richard P. Beyer, Ph.D. University of Washington >> Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 >> Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 >> Seattle, WA 98105-6099 >> http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html >> http://staff.washington.edu/~dbeyer >> ******************************************************************* ************ >> >> >> >> >> _______________________________________________ >> 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 > > > -- > Martin Morgan > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793 >
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Hi Dick, FYI: the R-package of IntegrOmics is available through CRAN: http://cran.r-project.org/web/packages/integrOmics/index.html G ------------------------------------------------ Guido Hooiveld, PhD Nutrition, Metabolism & Genomics Group Division of Human Nutrition Wageningen University Biotechnion, Bomenweg 2 NL-6703 HD Wageningen the Netherlands tel: (+)31 317 485788 fax: (+)31 317 483342 internet: http://nutrigene.4t.com email: guido.hooiveld at wur.nl > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch > [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of > Dick Beyer > Sent: 22 February 2010 02:05 > To: Martin Morgan > Cc: Bioconductor > Subject: Re: [BioC] Bioconductor Digest, Vol 84, Issue 19 > > Hi Martin, > > Thanks for the excellent pointer to PMA. (Sorry about the > poor choice of subject lines. Very nice of you to respond!) > > Thanks very much, > Dick > ************************************************************** > ***************** > Richard P. Beyer, Ph.D. University of Washington > Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 > Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 > Seattle, WA 98105-6099 > http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html > http://staff.washington.edu/~dbeyer > ************************************************************** > ***************** > > On Sat, 20 Feb 2010, Martin Morgan wrote: > > > On 02/19/2010 11:51 AM, Dick Beyer wrote: > >> I was wondering if anyone is working on OMICS integration? > >> Specifically, integrating data from gene expression, > proteomics, and > >> metabolomics for the same samples. > >> > >> I know about integrOmics: > >> > >> KL Cao, I Gonz?lez, S D?jean, integrOmics: an R package to unravel > >> relationships between two omics datasets, BIOINFORMATICS > APPLICATIONS > >> NOTE Vol. 25 no. 21 2009, pages 2855-2856 > >> > >> but that package is not yet available. > > > > Speaking a little out of my comfort zone, but > > > > http://cran.r-project.org/web/packages/PMA/index.html > > > > as a statistical methodology seems well motivated. > > > > Martin > > > >> > >> Thanks very much, > >> Dick > >> > ********************************************************************* > >> ********** > >> > >> Richard P. Beyer, Ph.D. University of Washington > >> Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 > >> Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 > >> Seattle, WA 98105-6099 > >> http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html > >> http://staff.washington.edu/~dbeyer > >> > ********************************************************************* > >> ********** > >> > >> > >> > >> > >> _______________________________________________ > >> 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 > > > > > > -- > > Martin Morgan > > Computational Biology / Fred Hutchinson Cancer Research Center 1100 > > Fairview Ave. N. > > PO Box 19024 Seattle, WA 98109 > > > > Location: Arnold Building M1 B861 > > Phone: (206) 667-2793 > > >
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Hi Guido, Thanks for the URL. Much appreciated. Dick ********************************************************************** ********* Richard P. Beyer, Ph.D. University of Washington Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 Seattle, WA 98105-6099 http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html http://staff.washington.edu/~dbeyer ********************************************************************** ********* On Mon, 22 Feb 2010, Hooiveld, Guido wrote: > > Hi Dick, > > FYI: the R-package of IntegrOmics is available through CRAN: > http://cran.r-project.org/web/packages/integrOmics/index.html > > G > > ------------------------------------------------ > Guido Hooiveld, PhD > Nutrition, Metabolism & Genomics Group > Division of Human Nutrition > Wageningen University > Biotechnion, Bomenweg 2 > NL-6703 HD Wageningen > the Netherlands > tel: (+)31 317 485788 > fax: (+)31 317 483342 > internet: http://nutrigene.4t.com > email: guido.hooiveld at wur.nl > > > >> -----Original Message----- >> From: bioconductor-bounces at stat.math.ethz.ch >> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of >> Dick Beyer >> Sent: 22 February 2010 02:05 >> To: Martin Morgan >> Cc: Bioconductor >> Subject: Re: [BioC] Bioconductor Digest, Vol 84, Issue 19 >> >> Hi Martin, >> >> Thanks for the excellent pointer to PMA. (Sorry about the >> poor choice of subject lines. Very nice of you to respond!) >> >> Thanks very much, >> Dick >> ************************************************************** >> ***************** >> Richard P. Beyer, Ph.D. University of Washington >> Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 >> Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 >> Seattle, WA 98105-6099 >> http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html >> http://staff.washington.edu/~dbeyer >> ************************************************************** >> ***************** >> >> On Sat, 20 Feb 2010, Martin Morgan wrote: >> >>> On 02/19/2010 11:51 AM, Dick Beyer wrote: >>>> I was wondering if anyone is working on OMICS integration? >>>> Specifically, integrating data from gene expression, >> proteomics, and >>>> metabolomics for the same samples. >>>> >>>> I know about integrOmics: >>>> >>>> KL Cao, I Gonz?lez, S D?jean, integrOmics: an R package to unravel >>>> relationships between two omics datasets, BIOINFORMATICS >> APPLICATIONS >>>> NOTE Vol. 25 no. 21 2009, pages 2855-2856 >>>> >>>> but that package is not yet available. >>> >>> Speaking a little out of my comfort zone, but >>> >>> http://cran.r-project.org/web/packages/PMA/index.html >>> >>> as a statistical methodology seems well motivated. >>> >>> Martin >>> >>>> >>>> Thanks very much, >>>> Dick >>>> >> ********************************************************************* >>>> ********** >>>> >>>> Richard P. Beyer, Ph.D. University of Washington >>>> Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 >>>> Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 >>>> Seattle, WA 98105-6099 >>>> http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html >>>> http://staff.washington.edu/~dbeyer >>>> >> ********************************************************************* >>>> ********** >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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 >>> >>> >>> -- >>> Martin Morgan >>> Computational Biology / Fred Hutchinson Cancer Research Center 1100 >>> Fairview Ave. N. >>> PO Box 19024 Seattle, WA 98109 >>> >>> Location: Arnold Building M1 B861 >>> Phone: (206) 667-2793 >>> >> > >
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