[Bioc-devel] ifnotfound in mget

Seth Falcon sfalcon at fhcrc.org
Fri Sep 1 21:04:24 CEST 2006

Francois Pepin <fpepin at aei.ca> writes:
> Yes, filtering is essential for many analyses. Not doing any can be a
> useful sanity check in many cases, for example in differential
> expression or looking for batch effects.
> The issue with the ifnotfound is it will call stop if an unknown probe
> is put in the mix:
>> args(mget)
> function (x, envir, mode = "any", ifnotfound = list(function(x) stop
> (paste("value for '",x, "' not found", sep = ""), call. = FALSE)),
> inherits = FALSE)

> I would like if the control were treated as probes that do not map to
> anything instead of evil things that make code crash.

If you send a patch, we'll review it :-)
In many cases, it seems to me that raising an error is the best
thing.  In general, I prefer errors to warnings.  Warnings one tends
to ignore until you discover you really shouldn't have ignored them.
Errors make you fix your mess right away.

> I'd agree its probably not very high in the list of priorities, as the
> workaround is pretty trivial (ie filter control probes).

We agree on this.

+ seth

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