'Re: [BioC] R: CORNA and biomaRt packages. miRNA and mRNA expression'

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List:       bioconductor
Subject:    Re: [BioC] R: CORNA and biomaRt packages. miRNA and mRNA expression
From:       Jordi Altirriba <altirriba () hotmail ! com>
Date:       2010-11-26 9:55:40
Message-ID: BLU103-W575CD208E4E4C2CA00270B5210 () phx ! gbl
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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 \
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> > 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.1252;LC_MONETARY=French_Switzerland.1252;LC_NUMERIC=C;LC_TIME=French_Switzerland.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 
> > 
> > _______________________________________________
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> 
> 
> -- 
> 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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