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@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 [[alternative HTML version deleted]]

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 [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor 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