[BioC] DEseq version and R version compatibility

[Wolfgang Huber]

Dear Jose Luis

please either convince your sys admin to install the current release version of R (2.15.1) and Bioconductor (2.11), or install it privately on the server e.g. in your home directory (it is easy). Everything else leads to insanity. 

Note that each R package (incl. DESeq) comes with its documentation, and it is versioned by a version number rather than calendar dates. The presence of outdated PDFs somewhere in the internet does not mean that you should these.

	Best wishes
	Wolfgang

Il giorno Oct 4, 2012, alle ore 4:41 PM, Thomas Girke <thomas.girke at ucr.edu> ha scritto:

> 
> There is no good reason not to keep R and Bioc fully up-to-date on a
> Linux server for all users while maintaining older versions too. If they
> have certain dependencies then one can easily configure things that
> users can call a specific R version by its version number, e.g. calling
> the latest version by typing R-2.15.2 instead of just R. A more generic
> solution to this is usually to use a module system that administers
> versions of any software not just R: http://modules.sourceforge.net/.
> This can be extremely useful in the NGS analysis world since you will
> end up installing new versions of all kinds of software (e.g. aligners,
> assemblers, Perl/Python modules) almost every day. 
> 
> Thomas
> 
> 
> On Thu, Oct 04, 2012 at 12:24:46PM +0000, José Luis Lavín wrote:
>> Dear all,
>> 
>> First of all I'd like to apologize for bothering you with such a naive
>> question, but I've been told that this is the place to ask about this
>> particular issue.
>> 
>> I'm trying to perform a Differential Expresion analysis on some RNA-seq
>> experiments using DEseq package. I'm not very fluent with R yet, and I'm
>> facing some problems while using DEseq for the analysis. In my institution
>> the R version of the Linux servers system is 2.13.0 and the version I
>> installed in my windows terminal is 2.15.2.
>> I've retrieved multiple DEseq manual versions from the internet (dated
>> 19/01/2010, 21/04/2011 and 12/04/2012) , but some R commands vary from one
>> to another and some are not supported in one or the other R versions I have
>> available. I need the R script to work in both versions and I don't really
>> know how to achieve it...
>> Could you please help me solving this giving me some kind of advice on how
>> to get a functional and compatible script to be used with both R versions I
>> previously stated?
>> 
>> Thanks in advance for your kind support.
>> 
>> With best wishes
>> 
>> JL
>> 
>> -- 
>> -- 
>> Dr. José Luis Lavín Trueba
>> 
>> Dpto. de Producción Agraria
>> Grupo de Genética y Microbiología
>> Universidad Pública de Navarra
>> 31006 Pamplona
>> Navarra
>> SPAIN
>> 
>> 	[[alternative HTML version deleted]]
>> 
> 
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