[BioC] Problem with Bimap objects

[axel.klenk at actelion.com]

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. :-)

Cheers,

 - axel


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




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



Hi,



I am trying to run an Hypergeometric test from Agilent mouse array. In my 
first
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



>sessionInfo()

R version 2.12.1 (2010-12-16)

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



locale:

[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 
a
simple one or difficult one, but I'm learning as I go and am a bit lost at 
this
point.



Thanks,



Lola Guerrero


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