[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. :-)
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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