[Bioc-sig-seq] using DEXSeq for RNA-seq data from Linux
Martin Morgan
mtmorgan at fhcrc.org
Mon Jul 25 14:13:16 CEST 2011
On 07/25/2011 02:28 AM, Jane Merlevede wrote:
> Hello,
>
> As you advise me, I installed R version 2.14 but I can't use the DEXSeq
> library: package "‘DEXSeq’ is not available (for R Under
> development)"... Do you know why?
It's a Bioconductor package, installed the Bioconductor way,
http://bioconductor.org/install/
that is,
source("http://bioconductor.org/biocLite.R")
biocLite("DEXSeq")
library(DEXSeq)
Glad the installation went ok, and I think DEXSeq will install correctly
for you.
Usually the 'devel' branch of R is quite stable, but actually just at
the moment there is some instability and you might experience problems
when trying to install or load some package combinations. One error
message is
Error in function (classes, fdef, mtable) :
unable to find an inherited method for function "[", for signature
"signature"
Error: loading failed
and unfortunately the only really accessible solution, if you encounter
this at a crucial stage of your analysis, is to wait a few days and
update your R.
Martin
> Thanks,
> Jane
>
>
> >R.2.14
>
> R Under development (unstable) (2011-07-24 r56492)
> Copyright (C) 2011 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> R est un logiciel libre livré sans AUCUNE GARANTIE.
> Vous pouvez le redistribuer sous certaines conditions.
> Tapez 'license()' ou 'licence()' pour plus de détails.
>
> R est un projet collaboratif avec de nombreux contributeurs.
> Tapez 'contributors()' pour plus d'information et
> 'citation()' pour la façon de le citer dans les publications.
>
> Tapez 'demo()' pour des démonstrations, 'help()' pour l'aide
> en ligne ou 'help.start()' pour obtenir l'aide au format HTML.
> Tapez 'q()' pour quitter R.
>
> > install.packages("DEXSeq")
> --- SVP sélectionner un miroir CRAN pour cette session ---
> CRAN mirror
>
> 1: Argentina (La Plata) 2: Argentina (Mendoza)
> 3: Australia (Canberra) 4: Australia (Melbourne)
> 5: Austria 6: Belgium
> 7: Brazil (PR) 8: Brazil (RJ)
> 9: Brazil (SP 1) 10: Brazil (SP 2)
> 11: Canada (BC) 12: Canada (NS)
> 13: Canada (ON) 14: Canada (QC 1)
> 15: Canada (QC 2) 16: Chile
> 17: China (Beijing 1) 18: China (Beijing 2)
> 19: China (Hefei) 20: China (Hong Kong)
> 21: China (Xiamen) 22: Colombia (Bogota)
> 23: Colombia (Cali) 24: Denmark
> 25: France (Toulouse) 26: France (Lyon 1)
> 27: France (Lyon 2) 28: Germany (Berlin)
> 29: Germany (Goettingen) 30: Germany (Muenchen)
> 31: Germany (Wiesbaden) 32: Greece
> 33: Indonesia 34: Iran
> 35: Ireland 36: Italy (Milano)
> 37: Italy (Padua) 38: Italy (Palermo)
> 39: Japan (Hyogo) 40: Japan (Tsukuba)
> 41: Korea 42: Mexico (Mexico City)
> 43: Mexico (Texcoco) 44: Netherlands (Amsterdam)
> 45: Netherlands (Utrecht) 46: New Zealand
> 47: Norway 48: Philippines
> 49: Poland (Gdansk) 50: Poland (Oswiecim)
> 51: Poland (Wroclaw) 52: Russia
> 53: Singapore 54: Slovakia 1
> 55: Slovakia 2 56: South Africa
> 57: Spain (Madrid) 58: Sweden
> 59: Switzerland 60: Taiwan (Taichung)
> 61: Taiwan (Taipei 1) 62: Taiwan (Taipei 2)
> 63: Thailand 64: UK (Bristol)
> 65: UK (London) 66: UK (St Andrews)
> 67: USA (AZ) 68: USA (CA 1)
> 69: USA (CA 2) 70: USA (IA)
> 71: USA (MA) 72: USA (MI)
> 73: USA (MO) 74: USA (OH)
> 75: USA (OR) 76: USA (PA 1)
> 77: USA (PA 2) 78: USA (TX 1)
> 79: USA (TX 2) 80: USA (WA 1)
> 81: USA (WA 2)
>
> Sélection : 26
> Message d'avis :
> In getDependencies(pkgs, dependencies, available, lib) :
> package ‘DEXSeq’ is not available (for R Under development)
> >
>
>
>
> 2011/7/24 Martin Morgan <mtmorgan at fhcrc.org <mailto:mtmorgan at fhcrc.org>>
>
> On 07/22/2011 07:40 AM, Jane Merlevede wrote:
>
> Hello,
>
> I have used DESeq for gene differential expression analysis and
> I would like
> to use DEXSeq now for exon differential expression analysis.
> The point is that the library DEXSeq seems to be available only
> in R version
> 2.14.0 (unstable). I am working on Linux (CentOS), with R
> version 2.13.0. I
> have not found this R version 2.14.0 for Linux... Finally, I
> cannot use
> DEXSeq.
> I would like to know if DEXSeq will be soon available in R
> version 2.13.0.
> Or is the only solution to work with Windows?
>
>
> As Sean mentions, this requires R-devel. It is not that difficult to
> build R from source on Linux, see sections 1 and 2 of
>
> http://cran.fhcrc.org/doc/__manuals/R-admin.html
> <http://cran.fhcrc.org/doc/manuals/R-admin.html>
>
> The source code is available here
>
> http://cran.fhcrc.org/sources.__html
> <http://cran.fhcrc.org/sources.html>
>
> you are looking for R-devel.tar.gz
>
> Martin
>
>
> Thank you for your help,
> Jane Merlevède
>
> [[alternative HTML version deleted]]
>
>
>
>
> _________________________________________________
> Bioc-sig-sequencing mailing list
> Bioc-sig-sequencing at r-project.__org
> <mailto:Bioc-sig-sequencing at r-project.org>
> https://stat.ethz.ch/mailman/__listinfo/bioc-sig-sequencing
> <https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing>
>
>
>
> --
> Computational Biology
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
>
> Location: M1-B861
> Telephone: 206 667-2793
>
>
--
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
Location: M1-B861
Telephone: 206 667-2793
More information about the Bioc-sig-sequencing
mailing list