[BioC] mget() error with NA values

Hervé Pagès hpages at fhcrc.org
Thu Apr 30 19:16:01 CEST 2009

Hi Christian,

Christian Kohler wrote:
> thanks so much for your quick reply, but to be honest I still do not
> understand, why my function-call ( unique(unlist(mget(x,
> env=hgu133plus2ENTREZID,ifnotfound=NA))) ) produces 'NA' instead of the
> error-message above. 

Without having your sessionInfo(), we won't be able to tell either...

> The interesting thing is, that if I analyse exactly the same data with
> 2.3 as well as with 2.4, the analysis does not break with 2.3 but with
> 2.4 !?.
> Well, I guess the solution is somewhat simple :-)

If that means you are going to stick with 2.3 then yes, it's a simple
solution, but please note that 2.3 is not supported anymore and that
the annotations in 2.4 are much more recent and supposedly more accurate.
The small code modification suggested by Jim is really straightforward
and a better way to go IMO. And as an extra benefit, other people
will be able to run your pipeline and reproduce your results (the
current code is expected to break for anybody with a standard


> All the best,
> Christian

Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319

More information about the Bioconductor mailing list