[Bioperl-l] Microarray ANOVA module

[Ewan Birney]

On Tue, 13 Aug 2002 lsprilus@bioinformatics.weizmann.ac.il wrote:

> According to Robinson, Peter:
> > I would like to ask about the status of Bioperl's plans for modules for microarray data analysis. I have written a module that does ANOVA (F test) analysis of microarray ...
> 
> We are working on Bio::Maxd, a module for managing and accessing maxdSQL, the relational 
> implementation by Manchester Bioinformatics of the ArrayExpress schema developed 
> by the EBI.

Cool. 


What I would love to see is some discussion of the "business objects" and 
interfaces - by business objects I mean objects which are indepdent of 
whether they were built by files/databases/xml/whatever, for example, one 
might have:

  (these are all made up things)

  # assumming these are all interface definitions

  Bio::Array::PhysicalDescriptionI    # which points go to which elements
     ::Array::ElementI                # what is actually on the array
     ::Array::ExperimentDescriptionI  # description of an experiment
     ::Array::CapturedExperimentI     # A set of data, with a 
                                      # PhysicalDescriptionI and a 
                                      # ExperimentDescriptionI, and of 
                                      # course the data values!



Of course, ArrayExpress and friends are MIAMI compliant and MAGE-ML based,
both of which are clearl things to support, but I strongly believe that
the full MAGE-ML model should not be exposed as just "400 objects you
might want to use for describing array experiments" but instead mapped to
some clear cut interfaces and hide the complexity sensibly (eg, one might
have)


   Bio::Array::MAGEML::DataValue
                     ::TemperatureValue


etc


or indeed, have this outside of the Bio:: namespace as MAGEML may 
auto-generate the objects and one just needs to write bridging cases to 
the interfaces that we should agree on.



I am not a pro here, so I'd be interested in anyone's thoughts, but of 
course, we need to discuss how this should work inside bioperl as much as 
possible/sensible so groups have a common framework/concept set to work 
from







> 
> It allows data loading and retrieval from/to mysql. At this time it knows of
> Affimetrix data format for loading, and reports to files able to be analyzed 
> by GeneSpring.
> 
> Jaim
> -- 
>  Dr Jaime Prilusky                | Jaime.Prilusky@weizmann.ac.il
>  Weizmann Institute of Science    | fax: 972-8-9344113
>  76100 Rehovot - Israel           | tel: 972-8-9344959
> 
>  info URL http://bioinformatics.weizmann.ac.il/jaime_prilusky.html
>  OCA is at http://bioinformatics.weizmann.ac.il:8500
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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
<birney@ebi.ac.uk>. 
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