[Bioperl-l] microarrays and matrices

[Allen Day]

> I actually like Bio::Expression::*

Yes, me too, so that's where the modules are sitting.  My current work 
looks like this:

Bio::Expression::Probe
Bio::Expression::Probeset
Bio::Expression::Affymetrix
Bio::Expression::Affymetrix::Cel
Bio::Expression::Affymetrix::CDF

I'm adding PDL constructors for those inclined to use them, and for those 
who aren't... they don't have to.  What should be done with Makefile.PL if 
I have some code (not exactly) like:

sub asPDL {
  my(@args) = @_;
  eval{require PDL};
  die "ack!" if $@;
  return pdl @args;
}

Should a PDL requirement be placed in Makefile.PL or not?

-Allen


On Wed, 28 Aug 2002, Hilmar Lapp wrote:

> I actually like Bio::Expression::*
> 
> 	-hilmar
> 
> On Friday, August 23, 2002, at 11:15  AM, Allen Day wrote:
> > 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
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
> >
> --
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp at gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> -------------------------------------------------------------
> 
> 
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