[BioC] Problem with Bimap objects

axel.klenk at actelion.com axel.klenk at actelion.com
Wed Mar 7 15:16:15 CET 2012

Dear Lola,

the error is thrown because mget() cannot find an ENTREZ ID for 
"A_55_P2045896" in mgug4122a.db.

I think you can get mget to silently ignore that by adding ifnotfound = NA 
to your mget call, eg.

>entrezIds<-mget(featureNames(eset_sample1),  mgug4122aENTREZID, 
ifnotfound = NA)

but the reason it is not found is that (AFAICT) your oligo ID is from a 
more recent Agilent array and you
may have more luck using the annotation package MmAgilentDesign026655.db 
instead of mgug4122a.db.

And BTW, your R/Bioconductor version is more than a year old and updating 
it is always a good idea. :-)


 - axel

Axel Klenk
Research Informatician
Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil / 

Lola Guerrero <dolores.guerrero at caubet-cimera.es>
"bioconductor at r-project.org" <bioconductor at r-project.org>
07.03.2012 14:51
[BioC] Problem with Bimap objects
Sent by:
bioconductor-bounces at r-project.org


I am trying to run an Hypergeometric test from Agilent mouse array. In my 
step, working  on the non-specific filtering by removing probe sets that 
have no
Entrez Gene identifier I found the following error:

>entrezIds<-mget(featureNames(eset_sample1),  mgug4122aENTREZID)

Error in .checkKeys(value, Lkeys(x), x at ifnotfound) :

  value for "A_55_P2045896" not found


R version 2.12.1 (2010-12-16)

Platform: i386-pc-mingw32/i386 (32-bit)


[1] LC_COLLATE=Spanish_Spain.1252  LC_CTYPE=Spanish_Spain.1252

[3] LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C

[5] LC_TIME=Spanish_Spain.1252

attached base packages:

[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:

 [1] genefilter_1.32.0    annotate_1.28.1      GOstats_2.16.0

 [4] graph_1.28.0         Category_2.16.1      GO.db_2.4.5

 [7] mgug4122a.db_2.4.5   org.Mm.eg.db_2.4.6   RSQLite_0.9-4

[10] DBI_0.2-5            AnnotationDbi_1.12.0 Biobase_2.10.0

loaded via a namespace (and not attached):

[1] GSEABase_1.12.2 RBGL_1.28.0     splines_2.12.1  survival_2.36-2

[5] tools_2.12.1    XML_3.2-0.2     xtable_1.6-0

Could anyone help me? I'm new to this world and don't know if the error is 
simple one or difficult one, but I'm learning as I go and am a bit lost at 


Lola Guerrero

                 [[alternative HTML version deleted]]

Bioconductor mailing list
Bioconductor at r-project.org
Search the archives: 

The information of this email and in any file transmitted with it is strictly confidential and may be legally privileged.
It is intended solely for the addressee. If you are not the intended recipient, any copying, distribution or any other use of this email is prohibited and may be unlawful. In such case, you should please notify the sender immediately and destroy this email.
The content of this email is not legally binding unless confirmed by letter.
Any views expressed in this message are those of the individual sender, except where the message states otherwise and the sender is authorised to state them to be the views of the sender's company. For further information about Actelion please see our website at http://www.actelion.com

More information about the Bioconductor mailing list