[Bioperl-l] bioperl-microarray: status?

Chris Fields cjfields at uiuc.edu
Wed Apr 16 11:00:51 EDT 2008


That would be worth looking into at some point, if anyone's interested  
(though it may be best to build a 'bridging' module).  Wonder if it  
uses BioConductor and, if not, how performance is vs BioConductor?

chris

On Apr 16, 2008, at 6:36 AM, Heikki Lehvaslaiho wrote:

> FYI,
>
> Christoper Jones has just published
> [http://bioinformatics.oxfordjournals.org/cgi/content/short/ 
> 24/8/1102 an
> article in Bioinformatics] about his
> [http://search.cpan.org/perldoc?Microarray Microarray perl module]  
> in CPAN.
>
> (The text added into BioPerl wiki.)
>
> 	-Heikki
>
>
> On Friday 26 January 2007 16:05:01 Chris Fields wrote:
>> Don't know if it's worth it, but could the microarray package be
>> modified so that it deals with data generated from or interacts
>> directly with Bioconductor (i.e. maybe including some specialized
>> bioperl-run set of classes to run Bioconductor tasks, return
>> lightweight bioperl microarray classes)?  Allen pointed out in a
>> previous post that Bioconductor is the best pick for certain tasks,
>> while Perl excels at others:
>>
>> http://article.gmane.org/gmane.comp.lang.perl.bio.general/13993
>>
>> Might be nice if we could merge both strengths together in some way.
>>
>> chris
>>
>> On Jan 26, 2007, at 7:26 AM, Jay Hannah wrote:
>>> On Jan 25, 2007, at 2:30 AM, Allen Day wrote:
>>>> Eh, there is some discussion activity on the list, but not much.   
>>>> You
>>>> are really better off moving to Bioconductor.
>>>
>>> Ok, thanks. I added that to the wiki page:
>>>
>>>    http://www.bioperl.org/wiki/Microarray_package
>>>
>>> j
>>> seqlab.net
>>> http://www.bioperl.org/wiki/User:Jhannah
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> Christopher Fields
>> Postdoctoral Researcher
>> Lab of Dr. Robert Switzer
>> Dept of Biochemistry
>> University of Illinois Urbana-Champaign
>>
>>
>>
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>
>
>
> -- 
> ______ _/      _/_____________________________________________________
>      _/      _/
>     _/  _/  _/  Heikki Lehvaslaiho    heikki at_sanbi _ac _za
>    _/_/_/_/_/  Senior Scientist    skype: heikki_lehvaslaiho
>   _/  _/  _/  SANBI, South African National Bioinformatics Institute
>  _/  _/  _/  University of Western Cape, South Africa
>     _/      Phone: +27 21 959 2096   FAX: +27 21 959 2512
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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