[Bioperl-l] microarrays and matrices

[Allen Day]

There's been an off-list conversation going on about how to represent 
microarray data in bioperl.  I'm currently writing some modules to work 
with Affymetrix data, and they use PDL (perl data language) to store probe 
values and other information in a matrix.

Because of the concern of bioperl having too many external dependencies, 
it might not be a good idea to require PDL per se, but to have a matrix 
interface class that chooses how to implement the data structures 
internally, either with regular perl arrays or with PDL structures.

So the question is: what does a matrix class need to be able to do?

--

There is also the issue of where in the namespace hierarchy to put 
microarray classes.  So far suggested have been:

Bio::Microarray::*
Bio::Functional::Expression::Microarray::*  #whew!
Bio::Expression::Microarray::*
Bio::Experimental::Microarray::*
Bio::Assay::Microarray::*

Jason has made a valid point that we want to be able to put things like
SAGE, northerns, and microarrays all as daughters of a common namespace,
so that eliminates Bio::Microarray::*.  Are there any other namespace
suggestions, or other input people would like to make?


-Allen