[Bioc-sig-seq] using DEXSeq for RNA-seq data from Linux

[Martin Morgan]

On 07/25/2011 05:13 AM, Martin Morgan wrote:
> 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.

Actually, a solution is to build R from a snapshot several days ago, 
before 2011-07-21 from

ftp://ftp.stat.math.ethz.ch/Software/R

Martin

>
> 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]]
>>
>>
>>
>>
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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
>>
>>
>
>


-- 
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109

Location: M1-B861
Telephone: 206 667-2793