[Bioc-devel] eSet questions

Kasper Daniel Hansen khansen at stat.Berkeley.EDU
Sun Aug 21 07:24:16 CEST 2005

I have a few questions regarding the eSet class. According to the  
documentation (comments/help files) it is meant to replace the  
exprSet class, so I am wondering whether I should this this as the  
building block for a new class.

Basically I just need a matrix linked in the usual way to a phenoData  
slot (plus some more), so the standard approach would be to use an  
exprSet (and ignoring the se.exprs slot), and this is indeed what I  
have been doing in the first development.

Now I see that the oligo package is using the eSet class as the basic  
building block.

I do have some hesitations regarding using the eSet class as I do not  
see a lot of validity checking going on: eq. nothing ensures that the  
construction has an exprs slot (ok, not slot but member of the  
exprsListNM slot of the eList slot of the eSet object). In fact, even  
thought he comments indicate that the members of the exprListNM slot  
have the same dimension, nothing ensures this. Of course this could  
be solved by me using an appropriate validity function, but that  
seems a bit backwards to me (but that may be the intentions?)

In fact I would be tempted to use a new class like the exprSet  
without the se.exprs slot... (although I will probably opt for the  
exprSet class just for consistency).



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