[Bioperl-l] The Power of R

[Dr. T. I. Simpson]

I did use RSPerl but was deeply displeased with what was simply a solution  
born of necessity at the time. It got the job done, but was not a long  
term solution. I look likely to revisit the throny issue in the next  
couple of months as I am trying to package up some simple downstream  
clustering analysis code into a bioperl package. I would dearly love to  
have it all nicely connected up to R, so am keeping an eye on the some  
threads that are running on BioC/BioPerl integration and the potential to  
use BioLib for this purpose http://biolib.open-bio.org/wiki/Main_Page. I  
know painfully little about this at the moment, but plan to gen up in the  
coming weeks.

Ian.

On Wed, 07 Jan 2009 15:19:44 -0000, Mark A. Jensen <maj at fortinbras.us>  
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
>>>>>>
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>>
>>
>>
>> -- 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.
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>>
>
>



-- 
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.