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

Thu Nov 25 16:33:17 CET 2010

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
> 
> 
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> 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: giovedì 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 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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