[Bioc-devel] ifnotfound in mget

[Seth Falcon]

Francois Pepin <fpepin at cs.mcgill.ca> writes:

> Hi everyone,
>
> is there a particular reason why there is no "ifnotfound = NA" arguments
> in most bioconductor functions regarding the chip annotations
> (findLargest in Category being one example)?

Isn't findLargest in the genefilter package?  Anyhow, I'll venture an
answer regarding ifnotfound behavior.

> It turns out that some chips (for example the Agilent ones) have a
> several features that do not get it in the annotation package.
>
> For example, hgug4112a (human whole genome array) and has 43931
> features, while the annotation package knows about 41000. The missing
> ones include the control probes as well as some truly obscure probes
> that are almost unannotatable.
>
> If it is in the 41k and no data is found, then mget will return an NA,
> so the "ifnotfound=NA" argument gives a proper behavior (except that no
> name is attached to it).
>
> It is a bit frustrating to have to filter those away before calling
> mget, or a function which calls it.
>
> Or maybe that would be considered a problem with the annotation
> packages? I still think that having mget calling stop whenever an
> unknown probe is used is pretty harsh (an NA and a warning would be more
> reasonable, I think).

While frustrating, doing careful filtering is an important step of
many analysis.  And for findLargest, I guess you are asking for
'na.rm', not ifnotfound.

What do others think?  Is this an issue that deserves solving with
extra arguments? 


+ seth