[Bioc-devel] Biobase / eSet changes for this release

Tue, Apr 18, 2006 12:28 PM

I'll implement EmptyMatrix. I will then update validity checking (and
other methods, as necessary) to allow for it in place of any/all
elements in a class. This will take a couple of days to get around to,
and in the mean time I'll talk with Robert and Seth about what
elements are actually in SnpSet; in some ways the EmptyMatrix idea
makes a more flexible approach (specifying several required slots,
e.g., expression, call, copyNumber, but usually functioning correctly
if these are occupied by EmptyMatrix) appealing.

It might help for a two-second overview of how 'expression' data might
be generally useful; I can see how call and copyNumber will feed into
'downstream' analyses.

Martin

Seth Falcon <sfalcon at fhcrc.org> writes:

Hi Rafa,

I'm going to answer out of order...

Rafael A Irizarry <ririzarr at jhsph.edu> writes:

2) It seems that in general we will be storing  an esimate (expression, 
calls, copynumber) and some kind of measure of uncertainty (SE for 
expression, p-value fo calls, etc..). However, a big chunk fo the apps 
will not use uncertainty. It would be a shame to have to store a matrix 
of NAs every single time. How hard would be to have eSet take NULL for 
some matrices? The validity check can look at everything that is not NULL.
Notice that the alternative is to define  a new class which means, in my 
case, Ill need two classes for every class Im defining or having a 
matrix of NAs, which, given the size of data these days, will be very 
inneficient.

I think we should define an EmptyMatrix class:

    setClass("EmptyMatrix", contains="matrix")

Why?  Because:

 * new("EmptyMatrix") is small (no elements) 
 * We can dispatch on it.  I think we might be able to get some
   propagation of empty similar to how NA works.  This can keep the
   code from having to do lots of explicit type checking.
 * NULL can happen by accident and should be an error.  EmptyMatrix
   won't just "appear" from a calculation.
 * It will also mean that these values could go in a proper slot of
   type "matrix" without having to create the matrixOrNull class
   union.

1) SNPset as it is will not be useful. As far as I know only Rob and me 
are  developing software that will use snpSet. Both of us need a slot 
for copynumber. Otherwise we will need to create a new class, which will 
be the only one used, and we wont get to use the name SnpSet.

There is something to be said for reserving the general class names
for things that will be general.  Perhaps it makes sense to choose a
slightly more specific name while sorting out the all-purpose use
cases.

Your RafaSnpSet can become SnpSet.  But if you start with SnpSet and
go off in a direction that is not useful to others, then there is no
easy fix.



+ seth

[Bioc-devel] Biobase / eSet changes for this release

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