CORNA and biomaRt packages. miRNA and mRNA expression comparation
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@jordi-altirriba-gutierrez-682
Last seen 5.7 years ago
Dear Bioconductor users, I am trying to work with CORNA.1.2. package to observe how miRNA regulates mRNA expression levels, as described in Wu X, Watson M, CORNA: testing gene lists for regulation by microRNAs, Bioinformatics. 2009 Mar 15;25(6):832-3. I have downloaded this package from the authors? webpage: http://corna.sourceforge.net/ Nevertheless, this package was compiled with a version previous than R.2.10.0, so I am not able to run it in R.2.12.0 version (current version). I have downloaded R.2.9.0 version and I am able to load CORNA package but biomaRt is not running (BioMart web service failed) [sessionInfo below]. It?s not a problem of BioMart web service, as in R.2.12.0 BioMart is running correctly. My questions: 1.- Is there any way to run BioMart in previous versions of R? (R.2.9.0 or previous) 2.- If it?s not possible, could I recompile CORNA package to run in R.2.12.0? How? 3.- Is there any other package to associate miRNA expression levels from microarrays with mRNA expression levels from other microarrays? (I am working with rats and mice and MMIA is not working with these species) Many thanks for your time and suggestions. Yours faithfully, Jordi Altirriba Laboratoire du M?tabolisme Centre M?dical Universitaire Geneve > sessionInfo() R version 2.9.0 (2009-04-17) i386-pc-mingw32 locale: LC_COLLATE=French_Switzerland.1252;LC_CTYPE=French_Switzerland.1252;LC _MONETARY=French_Switzerland.1252;LC_NUMERIC=C;LC_TIME=French_Switzerl and.1252 attached base packages: [1] tools stats graphics grDevices utils datasets methods base other attached packages: [1] CORNA_1.2 XML_2.5-1 GEOquery_2.8.0 RCurl_0.98-1 bitops_1.0-4.1 biomaRt_2.0.0 Biobase_2.4.1
miRNA biomaRt miRNA biomaRt • 1.4k views
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@manca-marco-path-4295
Last seen 10.2 years ago
Hi Jordi you may want to have a look at R documentation here ( http://cran.r-project.org/doc/manuals/R-admin.html#The-Windows-toolset ) and here ( http://cran.r-project.org/doc/manuals/R-admin.html . To obtain the tools necessary to build and install packages from source on Windows you will need to visit the page of Duncan Murdoch http://www.murdoch-sutherland.com/Rtools/ ...you can also try following small guides that other have written to describe their experience with the process, but in case of troubleshooting you will have to go back to the basics (the two links I have indicated at the beginning) http://www.biostat.wisc.edu/~kbroman/Rintro/Rwinpack.html Good luck! -- Marco Manca, MD University of Maastricht Faculty of Health, Medicine and Life Sciences (FHML) Cardiovascular Research Institute (CARIM) Mailing address: PO Box 616, 6200 MD Maastricht (The Netherlands) Visiting address: Experimental Vascular Pathology group, Dept of Pathology - Room5.08, Maastricht University Medical Center, P. Debyelaan 25, 6229 HX Maastricht E-mail: m.manca at maastrichtuniversity.nl Office telephone: +31(0)433874633 Personal mobile: +31(0)626441205 Twitter: @markomanka ********************************************************************** *********************************************** This email and any files transmitted with it are confidential and solely for the use of the intended recipient. It may contain material protected by privacy or attorney-client privilege. If you are not the intended recipient or the person responsible for delivering to the intended recipient, be advised that you have received this email in error and that any use is STRICTLY PROHIBITED. If you have received this email in error please notify us by telephone on +31626441205 Dr Marco MANCA ********************************************************************** *********************************************** ________________________________________ Da: bioconductor-bounces at stat.math.ethz.ch [bioconductor-bounces at stat.math.ethz.ch] per conto di Jordi Altirriba [altirriba at hotmail.com] Inviato: gioved? 25 novembre 2010 10.18 A: bioconductor at stat.math.ethz.ch Oggetto: [BioC] CORNA and biomaRt packages. miRNA and mRNA expression comparation Dear Bioconductor users, I am trying to work with CORNA.1.2. package to observe how miRNA regulates mRNA expression levels, as described in Wu X, Watson M, CORNA: testing gene lists for regulation by microRNAs, Bioinformatics. 2009 Mar 15;25(6):832-3. I have downloaded this package from the authors? webpage: http://corna.sourceforge.net/ Nevertheless, this package was compiled with a version previous than R.2.10.0, so I am not able to run it in R.2.12.0 version (current version). I have downloaded R.2.9.0 version and I am able to load CORNA package but biomaRt is not running (BioMart web service failed) [sessionInfo below]. It?s not a problem of BioMart web service, as in R.2.12.0 BioMart is running correctly. My questions: 1.- Is there any way to run BioMart in previous versions of R? (R.2.9.0 or previous) 2.- If it?s not possible, could I recompile CORNA package to run in R.2.12.0? How? 3.- Is there any other package to associate miRNA expression levels from microarrays with mRNA expression levels from other microarrays? (I am working with rats and mice and MMIA is not working with these species) Many thanks for your time and suggestions. Yours faithfully, Jordi Altirriba Laboratoire du M?tabolisme Centre M?dical Universitaire Geneve > sessionInfo() R version 2.9.0 (2009-04-17) i386-pc-mingw32 locale: LC_COLLATE=French_Switzerland.1252;LC_CTYPE=French_Switzerland.1252;LC _MONETARY=French_Switzerland.1252;LC_NUMERIC=C;LC_TIME=French_Switzerl and.1252 attached base packages: [1] tools stats graphics grDevices utils datasets methods base other attached packages: [1] CORNA_1.2 XML_2.5-1 GEOquery_2.8.0 RCurl_0.98-1 bitops_1.0-4.1 biomaRt_2.0.0 Biobase_2.4.1 _______________________________________________ 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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On 11/25/2010 01:33 AM, Manca Marco (PATH) wrote: > > > Hi Jordi you may want to have a look at R documentation here ( http://cran.r-project.org/doc/manuals/R-admin.html#The-Windows-toolset ) and here ( http://cran.r-project.org/doc/manuals/R-admin.html . > > > To obtain the tools necessary to build and install packages from source on Windows you will need to visit the page of Duncan Murdoch http://www.murdoch-sutherland.com/Rtools/ > > ...you can also try following small guides that other have written to describe their experience with the process, but in case of troubleshooting you will have to go back to the basics (the two links I have indicated at the beginning) > http://www.biostat.wisc.edu/~kbroman/Rintro/Rwinpack.html > > > Good luck! > > -- > Marco Manca, MD > University of Maastricht > Faculty of Health, Medicine and Life Sciences (FHML) > Cardiovascular Research Institute (CARIM) > > Mailing address: PO Box 616, 6200 MD Maastricht (The Netherlands) > Visiting address: Experimental Vascular Pathology group, Dept of Pathology - Room5.08, Maastricht University Medical Center, P. Debyelaan 25, 6229 HX Maastricht > > E-mail: m.manca at maastrichtuniversity.nl > Office telephone: +31(0)433874633 > Personal mobile: +31(0)626441205 > Twitter: @markomanka > > > ******************************************************************** ************************************************* > > This email and any files transmitted with it are confidential and solely for the use of the intended recipient. > > It may contain material protected by privacy or attorney-client privilege. If you are not the intended recipient or the person responsible for > > delivering to the intended recipient, be advised that you have received this email in error and that any use is STRICTLY PROHIBITED. > > If you have received this email in error please notify us by telephone on +31626441205 Dr Marco MANCA > > ******************************************************************** ************************************************* > ________________________________________ > Da: bioconductor-bounces at stat.math.ethz.ch [bioconductor-bounces at stat.math.ethz.ch] per conto di Jordi Altirriba [altirriba at hotmail.com] > Inviato: gioved? 25 novembre 2010 10.18 > A: bioconductor at stat.math.ethz.ch > Oggetto: [BioC] CORNA and biomaRt packages. miRNA and mRNA expression comparation > > Dear Bioconductor users, > I am trying to work with CORNA.1.2. package to observe how miRNA regulates mRNA expression levels, as described in Wu X, Watson M, CORNA: testing gene lists for regulation by microRNAs, Bioinformatics. 2009 Mar 15;25(6):832-3. > I have downloaded this package from the authors? webpage: http://corna.sourceforge.net/ > Nevertheless, this package was compiled with a version previous than R.2.10.0, so I am not able to run it in R.2.12.0 version (current version). > I have downloaded R.2.9.0 version and I am able to load CORNA package but biomaRt is not running (BioMart web service failed) [sessionInfo below]. > It?s not a problem of BioMart web service, as in R.2.12.0 BioMart is running correctly. > My questions: > 1.- Is there any way to run BioMart in previous versions of R? (R.2.9.0 or previous) Hi Jordi -- In 2.9.2 I biocLite('biomaRt') library(biomaRt) example(getBM) with success. The windows toolchain is not too bad to set up, so if the package is well enough designed Marco's pointers will be 'easy enough' to follow. Martin > sessionInfo() R version 2.9.2 (2009-08-24) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] biomaRt_2.0.0 loaded via a namespace (and not attached): [1] RCurl_0.98-1 tools_2.9.2 XML_2.5-1 > > 2.- If it?s not possible, could I recompile CORNA package to run in R.2.12.0? How? > 3.- Is there any other package to associate miRNA expression levels from microarrays with mRNA expression levels from other microarrays? (I am working with rats and mice and MMIA is not working with these species) > Many thanks for your time and suggestions. > Yours faithfully, > > Jordi Altirriba > Laboratoire du M?tabolisme > Centre M?dical Universitaire > Geneve > >> sessionInfo() > R version 2.9.0 (2009-04-17) > i386-pc-mingw32 > locale: > LC_COLLATE=French_Switzerland.1252;LC_CTYPE=French_Switzerland.1252; LC_MONETARY=French_Switzerland.1252;LC_NUMERIC=C;LC_TIME=French_Switze rland.1252 > attached base packages: > [1] tools stats graphics grDevices utils datasets methods base > other attached packages: > [1] CORNA_1.2 XML_2.5-1 GEOquery_2.8.0 RCurl_0.98-1 bitops_1.0-4.1 biomaRt_2.0.0 Biobase_2.4.1 > > > _______________________________________________ > 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 -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793
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Dear Martin and Morgan, Many thanks for your answers. It seems that something strange happens with my internet connection. biomaRt runs perfectly in R.2.12.0 but with R.2.9.0 or previous it doesn’t work. I have reinstalled R.2.9.0 in another computer from the University, but biomaRt also doesn’t work. Nevertheless, I have installed remotely in another computer from another country R.2.9.0 and biomaRt runs perfectly. Crazy But solved! Thanks! Jordi Altirriba Laboratoire du Métabolisme Centre Médical Universitaire Geneva > Date: Thu, 25 Nov 2010 07:33:17 -0800 > From: mtmorgan@fhcrc.org > To: m.manca@maastrichtuniversity.nl > CC: altirriba@hotmail.com; bioconductor@stat.math.ethz.ch > Subject: Re: [BioC] R: CORNA and biomaRt packages. miRNA and mRNA expression comparation > > On 11/25/2010 01:33 AM, Manca Marco (PATH) wrote: > > > > > > Hi Jordi you may want to have a look at R documentation here ( http://cran.r-project.org/doc/manuals/R-admin.html#The-Windows-toolset ) and here ( http://cran.r-project.org/doc/manuals/R-admin.html . > > > > > > To obtain the tools necessary to build and install packages from source on Windows you will need to visit the page of Duncan Murdoch http://www.murdoch-sutherland.com/Rtools/ > > > > ...you can also try following small guides that other have written to describe their experience with the process, but in case of troubleshooting you will have to go back to the basics (the two links I have indicated at the beginning) > > http://www.biostat.wisc.edu/~kbroman/Rintro/Rwinpack.html > > > > > > Good luck! > > > > -- > > Marco Manca, MD > > University of Maastricht > > Faculty of Health, Medicine and Life Sciences (FHML) > > Cardiovascular Research Institute (CARIM) > > > > Mailing address: PO Box 616, 6200 MD Maastricht (The Netherlands) > > Visiting address: Experimental Vascular Pathology group, Dept of Pathology - Room5.08, Maastricht University Medical Center, P. Debyelaan 25, 6229 HX Maastricht > > > > E-mail: m.manca@maastrichtuniversity.nl > > Office telephone: +31(0)433874633 > > Personal mobile: +31(0)626441205 > > Twitter: @markomanka > > > > > > ****************************************************************** *************************************************** > > > > This email and any files transmitted with it are confidential and solely for the use of the intended recipient. > > > > It may contain material protected by privacy or attorney-client privilege. If you are not the intended recipient or the person responsible for > > > > delivering to the intended recipient, be advised that you have received this email in error and that any use is STRICTLY PROHIBITED. > > > > If you have received this email in error please notify us by telephone on +31626441205 Dr Marco MANCA > > > > ****************************************************************** *************************************************** > > ________________________________________ > > Da: bioconductor-bounces@stat.math.ethz.ch [bioconductor- bounces@stat.math.ethz.ch] per conto di Jordi Altirriba [altirriba@hotmail.com] > > Inviato: giovedì 25 novembre 2010 10.18 > > A: bioconductor@stat.math.ethz.ch > > Oggetto: [BioC] CORNA and biomaRt packages. miRNA and mRNA expression comparation > > > > Dear Bioconductor users, > > I am trying to work with CORNA.1.2. package to observe how miRNA regulates mRNA expression levels, as described in Wu X, Watson M, CORNA: testing gene lists for regulation by microRNAs, Bioinformatics. 2009 Mar 15;25(6):832-3. > > I have downloaded this package from the authors’ webpage: http://corna.sourceforge.net/ > > Nevertheless, this package was compiled with a version previous than R.2.10.0, so I am not able to run it in R.2.12.0 version (current version). > > I have downloaded R.2.9.0 version and I am able to load CORNA package but biomaRt is not running (BioMart web service failed) [sessionInfo below]. > > It’s not a problem of BioMart web service, as in R.2.12.0 BioMart is running correctly. > > My questions: > > 1.- Is there any way to run BioMart in previous versions of R? (R.2.9.0 or previous) > > Hi Jordi -- In 2.9.2 I > > biocLite('biomaRt') > library(biomaRt) > example(getBM) > > with success. The windows toolchain is not too bad to set up, so if the > package is well enough designed Marco's pointers will be 'easy enough' > to follow. > > Martin > > > sessionInfo() > R version 2.9.2 (2009-08-24) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] biomaRt_2.0.0 > > loaded via a namespace (and not attached): > [1] RCurl_0.98-1 tools_2.9.2 XML_2.5-1 > > > > > > 2.- If it’s not possible, could I recompile CORNA package to run in R.2.12.0? How? > > 3.- Is there any other package to associate miRNA expression levels from microarrays with mRNA expression levels from other microarrays? (I am working with rats and mice and MMIA is not working with these species) > > Many thanks for your time and suggestions. > > Yours faithfully, > > > > Jordi Altirriba > > Laboratoire du Métabolisme > > Centre Médical Universitaire > > Geneve > > > >> sessionInfo() > > R version 2.9.0 (2009-04-17) > > i386-pc-mingw32 > > locale: > > LC_COLLATE=French_Switzerland.1252;LC_CTYPE=French_Switzerland.125 2;LC_MONETARY=French_Switzerland.1252;LC_NUMERIC=C;LC_TIME=French_Swit zerland.1252 > > attached base packages: > > [1] tools stats graphics grDevices utils datasets methods base > > other attached packages: > > [1] CORNA_1.2 XML_2.5-1 GEOquery_2.8.0 RCurl_0.98-1 bitops_1.0-4.1 biomaRt_2.0.0 Biobase_2.4.1 > > > > > > _______________________________________________ > > 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 > > > > _______________________________________________ > > 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 > > > -- > Computational Biology > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 > > Location: M1-B861 > Telephone: 206 667-2793 [[alternative HTML version deleted]]
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