Hi Andrew, You can also just get your symbols this way: library(mouse4302.db) library(org.Mm.eg.db) select( mouse4302.db, keys ="1449880_s_at", cols="SYMBOL", keytype="PROBEID") This query will give you a warning because your probe will match to multiple symbols, but it avoids the step of having to create a special bimap that is set to expose all probes 1st. Marc On 10/23/2012 09:06 AM, Andrew Yee wrote: > Thanks for the information, that's extremely helpful. > > Thanks, > Andrew > > On Tue, Oct 23, 2012 at 10:43 AM, James W. MacDonald<jmacdon at="" uw.edu=""> wrote: >> Hi Andrew, >> >> >> On 10/22/2012 10:58 PM, Andrew Yee wrote: >>> I know I've raised a similar issue in May 2009 concerning how >>> frequently the annotation packages are updated, and I imagine this >>> issue has been raised by others as well: >>> >>> For this probe set id, 1449880_s_at, I am having some difficulty >>> finding annotation information for it in the mouse4302.db. >>> >>> The Affymerix website has its gene symbol annotation as Bglap, and the >>> date of their annotation file is from July 2011 >>> >>> >>> https://www.affymetrix.com/analysis/netaffx/fullrecord.affx?pk=MOU SE430_2:1449880_S_AT#a_grade >>> >>> However, I can't seem to find a similar annotation in the mouse4302.db >>> annotation package. I was wondering if there was a simple explanation >>> for this, or perhaps I am doing something wrong. >> >> It's a simple explanation. This probeset targets multiple genes, and the >> default of the annotation packages is to only return data for probesets that >> target a single gene. This behavior is modifiable, however. >> >> What you have been getting is this: >> >>> get("1449880_s_at", mouse4302SYMBOL) >> [1] NA >> >> but we can allow multiple hits using toggleProbes(): >> >>> x<- toggleProbes(mouse4302SYMBOL, "multiple") >>> get("1449880_s_at", x) >> [1] "Bglap" "Bglap-rs1" "Bglap2" >> >> Best, >> >> Jim >> >> >> >>> Thanks, >>> Andrew >>> >>> sessionInfo() >>> >>> R version 2.15.0 Patched (2012-03-30 r58877) >>> Platform: x86_64-unknown-linux-gnu (64-bit) >>> >>> locale: >>> [1] C >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] mouse4302.db_2.7.1 org.Mm.eg.db_2.7.1 RSQLite_0.11.1 >>> DBI_0.2-5 >>> [5] AnnotationDbi_1.18.0 Biobase_2.16.0 BiocGenerics_0.2.0 >>> BiocInstaller_1.4.3 >>> >>> loaded via a namespace (and not attached): >>> [1] IRanges_1.14.2 stats4_2.15.0 tools_2.15.0 >>> >>> _______________________________________________ >>> 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 >> >> -- >> James W. MacDonald, M.S. >> Biostatistician >> University of Washington >> Environmental and Occupational Health Sciences >> 4225 Roosevelt Way NE, # 100 >> Seattle WA 98105-6099 >>