[BioC] Order of probesets in an exprSet

[lgautier@altern.org]

> Dear BioC people,
>
> I have a little technical question about how the order of the probesets
> in an exprSet is defined.
> Is this order given by the order of the probesets in the corresponding
> cdf environment (e.g. ls(mouse4302cdf))?
> Or is it alphabetical?
> Or is it "unconstrained"?
>
> In the examples I've looked at both the order of the probesets in the
> cdf environment and the exprSets are the same (and alphabetical).

There is probably no "order" in a cdf environment (in the sense
people think of it). This is a hash table, and the order in which
elements are returned depends on the implementation of it, and eventually
on the keys in the hash table.
I would suspect that R returns keys in alphabetical order (but I am not
sure of that, and therefore never -or should not- assume it blindly in my
code).

Having the same order (at least on the same platform) is implicit if you
used 'expresso' (or wrappers) without specifying a list of probe set IDs to
work with: an exprSet is then obtained by looping through all keys in the
cdfenv (and in the order these keys are returned, AFAIR).


Hoping this helps,


L.


> But is it a characteristic which is desired by development or is it just
> fortuitous?
>
> Thank you in advance for your insight...
> Adrien Jamain
>
>
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