[BioC] DEseq version and R version compatibility

[Sean Davis]

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]]
>> >
>> >
>> > _______________________________________________
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>>
>
>
>
> --
> --
> 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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