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

Wolfgang Huber huber at ebi.ac.uk
Tue Apr 18 18:32:39 CEST 2006

Hi Seth,

I like the idea of "EmptyMatrix".
Another more pedestrian option would be "matrix" x with
such as e.g. the result of new("matrix").

The only (small) advantage is that new users/developers that know R but 
not bioc might find it less intimidating if our designs are not overly 

I don't mind much, just a suggestion


> 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 
> I think we should define an EmptyMatrix class:
>     setClass("EmptyMatrix", contains="matrix")

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