[BioC] DEseq version and R version compatibility

Thu Oct 4 16:50:40 CEST 2012

Hej José!

Start R, load the DESeq library and type in:

vignette("DESeq")

that will get you the PDF version of the manual corresponding to your installed version.

Cheers,

---------------------------------------------------------------
Nicolas Delhomme

Genome Biology Computational Support

European Molecular Biology Laboratory

Tel: +49 6221 387 8310
Email: nicolas.delhomme at embl.de
Meyerhofstrasse 1 - Postfach 10.2209
69102 Heidelberg, Germany
---------------------------------------------------------------

On Oct 4, 2012, at 4:42 PM, José Luis Lavín wrote:

> Thank you everybody for your advice and opinions. I just wanted to be able
> to analyze my DE data and since I couldn't change R versions due to issues
> beyond my grasp...
> So, since I've the current R version in windows, I'll try to follow the
> newest manual commands there.
> ¿May any of you tell me which is the last version of  DEseq manual?
> I'll keep up trying to make DEseq work, since I believe it's the tool of
> choice for my work unless any of you may tell me about a different one that
> could be easier to use without losing DEseq superb analysis capabilities.
> 
> Thank you again for your time and attention.
> 
> With best wishes
> 
> JL
> 
> 2012/10/4 Sean Davis <sdavis2 at mail.nih.gov>
> 
>> On Thu, Oct 4, 2012 at 9:30 AM, José Luis Lavín <jluis.lavin at unavarra.es>
>> wrote:
>>> Hello Sean,
>>> 
>>> The main problem with updating the R version of the servers is that I'm
>> not
>>> the SysAdmin, and he told me that they couldn't update it at the moment
>>> because they have some processes and pipelines that need the old R
>> version
>>> (2.13), so he can't update it (weird, isn't it?). That's why I was
>> looking
>>> for such strange compatibility...
>>> Anyway, due to my current low level on R scripting, when I come across a
>>> command that isn't functional I don't really know what to do but trying
>> to
>>> use another manual version hoping the code there will fix it...but I've
>> had
>>> no luck with that at the moment. That's why I asked about this.
>>> I'll keep trying to make DEseq work, but I begin to feel stupid, reading
>>> everybody seems to be able to run it except myself.
>> 
>> If you have a good relationship with your sysadmin, ask him/her to
>> help you to install R in your home directory.  This is not hard to do
>> (hopefully, for a sysadmin) and will allow you to run a different
>> version of R than that already installed on the system.  Really, doing
>> this will be much better than copying code from various versions of
>> packages to "just make it work".
>> 
>> Sean
>> 
>> 
>>> Thank you for your swift answer, anyway
>>> 
>>> Best wishes
>>> 
>>> JL
>>> 
>>> 2012/10/4 Sean Davis <sdavis2 at mail.nih.gov>
>>> 
>>>> On Thu, Oct 4, 2012 at 8:24 AM, José Luis Lavín <
>> jluis.lavin at unavarra.es>
>>>> 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?
>>>> 
>>>> Hi, José.
>>>> 
>>>> The versions of DEseq are matched to the versions of bioconductor
>>>> which are matched to the versions of R.  In other words, the only way
>>>> to match the versions of DEseq between two machines is to use the same
>>>> version of R on both.  Installing R in your home directory is not
>>>> difficult, so I'd suggest you try that on your linux cluster since
>>>> R-2.13 is pretty outdated at this point.
>>>> 
>>>> Also, you'll want to ALWAYS use biocLite() to install packages, as
>>>> detailed on the bioconductor website.  This can avoid headaches with
>>>> version mismatches in the future.
>>>> 
>>>> Sean
>>>> 
>>>> 
>>>>> 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]]
>>>>> 
>>>>> 
>>>>> _______________________________________________
>>>>> Bioconductor mailing list
>>>>> Bioconductor at r-project.org
>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>> Search the archives:
>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>> 
>>> 
>>> 
>>> 
>>> --
>>> --
>>> 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]]
>>> 
>>> 
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>> 
> 
> 
> 
> -- 
> -- 
> 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]]
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor