[Bioperl-l] Fwd: [Bioperl-guts-l] [15134] bioperl-live/trunk/Bio/Microarray/Tools: use superclasses initialization and argument processing/ attribute setting as suggested in styleguide

Dr. T. I. Simpson ian.simpson at ed.ac.uk
Thu Dec 11 15:19:20 UTC 2008


Hi guys, I am a newbie on here so  hope this mail is appropriate.

Just thought I would chip in here (sorry for the pun). I would like to  
echo Marian's comments. I work extensively with R/BioC and Perl taking  
experimental data from low-level array to lots of different downstream  
analyses. I made an effort to work with R through Perl about a year ago  
using RSPerl and it was mighty painful. As Marian suggests it wouldn't be  
a good idea to compete with R/BioC there are some absolutely gold standard  
packages like affy, affyPLM and limma to name just three that cope with  
serious statistics within the R environment. If it were possible to make a  
good bridge to execute R scripts and access/manipulate R variables (a run  
wrapper  module for R ?) then that would be a very significant step  
forward for someone like me. I don't know how skillfully I could  
contribute to this, but happy to help wherever I can.

Best wishes

Ian.

On Thu, 11 Dec 2008 10:12:42 -0000, Marian thieme  
<Marian.thieme at klinik.uni-regensburg.de> wrote:

> I also had the impression that "it" was discouraged to use bioperl for  
> microarray processing.
> As I know from my colleagues and also I did to good extemt) people use R  
> (especially Bioconductor) for most of the issues concerning microarrays.  
> (there are so many supoorted microarray designs, preprocessing and  
> normalization tools, and complete packages to perform differential  
> expression analysis). At least for the expression chips but also for  
> genotyping/SNP chips I think R/BioC is method of choice. Probably for  
> the resequencing chips they are not that well supported, because its  
> only a minority that uses this kind of chips. Therefore I think  
> ReseqChip has its right to exist, even though it would reach more people  
> if it would a R/BioC package. (Moreover I believe that this kind of  
> chips wont have broader interest, because second generation sequencing  
> methods will probably be more appropriate in the next few years)
> So to cut a long story short, I find Chris' idea of bridging bioperl to  
> BioC (or vice versa) very good: Dont compete against R/BioC, but make it  
> easier to use both together.
>
> marian
>
> Marian Thieme
> Institute of Functional Genomics
> University Regensburg
> Josef Engert Str. 9
> 93053
> Regensburg
> Germany
> P: 0049 (0)941 943 1584
> F: 0049 (0)941 943 5020
> E:  marian.thieme at klinik.uni-regensburg.de
> W: http://www-cgi.uni-regensburg.de/Klinik/FunktionelleGenomik
>
>
>>>> Chris Fields <cjfields at illinois.edu> 12/10/2008 7:59 PM >>>
> Sounds like a good idea, with one caveat: Allen had pretty much given
> up on bioperl-microarray last I heard (last significant commits were
> ~6 yrs ago).  It would be nice to revive with this theme in mind,
> though maybe bioperl-expression would be better (could focus on other
> expression-related issues along with microarray data).  Marian, what
> do you think?
>
> chris
>
> P.S. An aside: I'm planning on running lots of Illumina data myself
> and have been thinking about making a BioC-BioPerl bridge, then seeing
> how it fits into a bioperl-microarray.  Just need a working perl-R
> interface (NOT RSPerl).
>
> On Dec 10, 2008, at 12:42 PM, Jason Stajich wrote:
>
>> Since we've started discussing the idea of starting to move things
>> out into smaller packages, does it make sense to move this
>> Bio::Microarray into its own package before it gets bigger? What
>> about the old bioperl-microarray stuff from Allen Day?
>>
>> I also know that as we haven't branched for 1.6 Chris we'll have to
>> make some decisions about new code going in before then?
>>
>> Not trying to stifle any of the development with extra work but
>> trying to see if we should start to make some logical slices of
>> packages?
>>
>> -jason
>>
>> Begin forwarded message:
>>
>>> From: Marian Thieme <thm09830 at dev.open-bio.org>
>>> Date: December 10, 2008 6:10:21 AM PST
>>> To: bioperl-guts-l at bioperl.org
>>> Subject: [Bioperl-guts-l] [15134] bioperl-live/trunk/Bio/Microarray/
>>> Tools: use superclasses initialization and argument processing/
>>> attribute setting as suggested in styleguide
>>>
>>> Revision: 15134
>>> Author:   thm09830
>>> Date:     2008-12-10 09:10:21 -0500 (Wed, 10 Dec 2008)
>>>
>>> Log Message:
>>> -----------
>>> use superclasses initialization and argument processing/attribute
>>> setting as suggested in styleguide
>>>
>>> Modified Paths:
>>> --------------
>>>   bioperl-live/trunk/Bio/Microarray/Tools/MitoChipV2Parser.pm
>>>   bioperl-live/trunk/Bio/Microarray/Tools/ReseqChip.pm
>>>
>>> Modified: bioperl-live/trunk/Bio/Microarray/Tools/MitoChipV2Parser.pm
>>> ===================================================================
>>> --- bioperl-live/trunk/Bio/Microarray/Tools/MitoChipV2Parser.pm	
>>> 2008-12-10 12:51:47 UTC (rev 15133)
>>> +++ bioperl-live/trunk/Bio/Microarray/Tools/MitoChipV2Parser.pm	
>>> 2008-12-10 14:10:21 UTC (rev 15134)
>>> @@ -78,12 +78,13 @@
>>>
>>> sub new {
>>>
>>> -  my ($class, $file_name) = @_;
>>> -  my $self = $class->SUPER::new();
>>> +  my ($class, @args) = @_;
>>> +  my $self = $class->SUPER::new(@args);
>>> +  my ($file_name)=$self->_rearrange([qw(AFFY_DESIGN_FILENAME)],
>>> @args);
>>> +
>>>  $self->{_frags_hash}=undef;
>>>  $self->{_oligos2calc_hash}=undef;
>>>  $self->throw("Must provide filename as first argument !") unless
>>> $file_name;
>>> -
>>>
>>>  my %max_ins_hash=();
>>>  $self->{_frags_hash}=$self-
>>> >_parse_Affy_mtDNA_design_annotation_file($file_name);
>>>
>>> Modified: bioperl-live/trunk/Bio/Microarray/Tools/ReseqChip.pm
>>> ===================================================================
>>> --- bioperl-live/trunk/Bio/Microarray/Tools/ReseqChip.pm	2008-12-10
>>> 12:51:47 UTC (rev 15133)
>>> +++ bioperl-live/trunk/Bio/Microarray/Tools/ReseqChip.pm	2008-12-10
>>> 14:10:21 UTC (rev 15134)
>>> @@ -194,8 +194,11 @@
>>>
>>> sub new {
>>>
>>> -  my ($class, $design_file_name, $format, $refseq_max_ins_hash,
>>> $refseq) = @_;
>>> -  my $self = $class->SUPER::new();
>>> +  #my ($class, $design_file_name, $format, $refseq_max_ins_hash,
>>> $refseq) = @_;
>>> +  my ($class, @args) = @_;
>>> +  my $self = $class->SUPER::new(@args);
>>> +  my ($design_file_name, $format, $refseq_max_ins_hash, $refseq)=
>>> $self->_rearrange([qw(AFFY_DESIGN_FILENAME FORMAT_OF_DESIGN_FILE
>>> MAX_INSERTION_HASH_REFERENCE REFERENCE_SEQUENCE)], @args);
>>> +
>>>  $self->{_frags_hash}=undef;
>>>  $self->{_max_ins_hash}=undef;
>>>  $self->{_refseq}=undef;
>>>
>>>
>>> _______________________________________________
>>> Bioperl-guts-l mailing list
>>> Bioperl-guts-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-guts-l
>>
>> Jason Stajich
>> jason at bioperl.org
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
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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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