[Bioperl-l] The Power of R

[Adam Witney]

We use it for one small, fairly simple application which was written  
by an MSc project student so allowed her to use Perl and R in her  
project. It was a bit of a pain to get up and running, but does the  
job and so is still in use. I'm not sure i would use it for anything  
more complicated though.

adam


On 7 Jan 2009, at 15:19, Mark A. Jensen wrote:

> What solution did you responders wind up using? Do people generally  
> get RSPerl to work and wash their hands of it afterwards? Or do you  
> finally hand-code a good deal? thx
> ----- Original Message ----- From: "Dr. T. I. Simpson" <ian.simpson at ed.ac.uk 
> >
> To: "Chris Fields" <cjfields at illinois.edu>; "Boris Umylny" <umylny at apbri.org 
> >
> Cc: <bioperl-l at lists.open-bio.org>
> Sent: Wednesday, January 07, 2009 9:55 AM
> Subject: Re: [Bioperl-l] The Power of R
>
>
>> I agree with Chris on this.
>>
>> Used RSPerl about a year ago to integrate some clustering  
>> experiments in R with a Perl script that fed data to R and picked  
>> up output, but it was  mighty painful and accessing R objects  
>> through RSPerl was indeed a PITA.
>>
>> Ian.
>>
>>
>> On Wed, 07 Jan 2009 13:26:14 -0000, Chris Fields <cjfields at illinois.edu 
>> > wrote:
>>
>>> Not to bash this, as it is a decent piece of software, but...  : >
>>>
>>> 1) Painful to install, and doesn't support a local perl  
>>> installation  (keeps attempting to go back and use my 5.8.8  
>>> instead of my local 5.10).
>>> 2) Not on CPAN.
>>> 3) Though this is supposed to be bidirectional, R from Perl is not  
>>> well supported and apparently does not work for Windows.
>>> 4) Doesn't appear to be well-supported in general.
>>>
>>> I do not intend on writing a full perl suite for R/BioC analyses  
>>> if I  end up having to work around problems with the critical  
>>> module.
>>>
>>> -c
>>>
>>> On Jan 6, 2009, at 11:34 PM, Boris Umylny wrote:
>>>
>>>> What do you think of RSPerl (http://www.omegahat.org/RSPerl/)?
>>>>
>>>>
>>>> Boris
>>>>
>>>>
>>>> ----- Original Message ----- From: "Chris Fields" <cjfields at illinois.edu
>>>> >
>>>> To: "Mark A. Jensen" <maj at fortinbras.us>
>>>> Cc: <bioperl-l at lists.open-bio.org>
>>>> Sent: Wednesday, January 07, 2009 2:04 PM
>>>> Subject: Re: [Bioperl-l] The Power of R
>>>>
>>>>
>>>>> Now if we can only get a decent Perl-R interface which isn't a  
>>>>> PITA to install...
>>>>>
>>>>> chris
>>>>>
>>>>> On Jan 6, 2009, at 9:33 PM, Mark A. Jensen wrote:
>>>>>
>>>>>> So says the New York Times:
>>>>>> http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>
>>
>>
>> -- 
>> Dr T. I. Simpson
>> School of Biomedical Sciences
>> University of Edinburgh
>> Hugh Robson Building
>> George Square
>> Edinburgh
>> EH8 9XD
>>
>> ian.simpson at ed.ac.uk
>>
>>
>> The University of Edinburgh is a charitable body, registered in
>> Scotland, with registration number SC005336.
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l