[Bioc-devel] assayDat and ExpressionSet

[Martin Morgan]

Kasper Daniel Hansen <khansen at stat.berkeley.edu> writes:

> There is currently (release version) no enforcement on whether an  
> ExpressionSet has one or more assayData members not called "exprs".  
> Is this intentional and will it be stable?

ExpressionSet assayData has to have exprs, but can have additional
members. 'Expression' is meant to imply summarized probe-set
expression values rather than raw probe-level intensities.

> Also, any particular reason why some of the validity functions like  
> validMsg (and some others as well) is not exported from Biobase? They  
> seem useful for validity tests.

The usual reasons of being a little ad hoc and experimental, and not
wanting to guarantee that they are permanent. Easy enough to export,
and unless I hear otherwise I'll do that. Others for export?

> Finally, as AffyBatch inherits from eSet there is no requirement (as  
> far as I can see) that an AffyData object has an "exprs" assayData  
> member. Shouldn't AffyBatch inherit from ExpressionSet (of course  
> that depends on the answer to my first question).

They're structurally similar but conceptually distinct; many of the
analyses you'd do on expression values would not make sense on raw
intensities. (Most of the functionality of ExpressionSet is inherited
from eSet).

This distinction is blurred by early use of 'exprs' for naming and
extracting the assayData element of AffyBatch; attempts to move away
from exprs generated confusion.

Probably several packages mis-use ExpressionSet.

You didn't ask, but probably AffyBatch should have a validity method
that checks for an appropriately dimensioned exprs element in
assayData.

Martin

> Kasper
>
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