[BioC] unable to find known entrezgene with biomaRt

[Dick Beyer]

Hello,

I am unable to find some Entrez Gene IDs in the ensembl homo sapiens database via biomaRt, even though I can access them via the ensembl web.

library(biomaRt)
mart <- useMart( "ensembl", dataset="hsapiens_gene_ensembl")

getBM(attributes=c("entrezgene","hgnc_symbol","ensembl_gene_id"),filters="entrezgene",values=3845, mart=mart)
   entrezgene hgnc_symbol ensembl_gene_id
1       3845        KRAS ENSG00000133703

getBM(attributes=c("entrezgene","hgnc_symbol","ensembl_gene_id"),filters="entrezgene",values=3514, mart=mart)
NULL

The ensembl web interface:

http://www.ensembl.org/Homo_sapiens/geneview?gene=ENSG00000211592

shows Entrez Gene ID 3514 corresponds to ensembl_gene_id ENSG00000211592, IGKC.

I'm curious why my biomaRt session will return good results for some valid Entrez Gene IDs but not for others.  I'm not sure what to try next.  I'd very much appreciate any help.

sessionInfo()
R version 2.6.1 (2007-11-26)
x86_64-redhat-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] tools     stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
  [1] topGO_1.4.0         SparseM_0.75        AnnotationDbi_1.0.6
  [4] RSQLite_0.6-4       DBI_0.2-4           GO_2.0.1
  [7] Biobase_1.16.2      graph_1.16.1        biomaRt_1.12.2
[10] RCurl_0.8-3

loaded via a namespace (and not attached):
[1] cluster_1.11.9  rcompgen_0.1-17 XML_1.93-2

Thanks much,
Dick
*******************************************************************************
Richard P. Beyer, Ph.D.	University of Washington
Tel.:(206) 616 7378	Env. & Occ. Health Sci. , Box 354695
Fax: (206) 685 4696	4225 Roosevelt Way NE, # 100
 			Seattle, WA 98105-6099
http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html
http://staff.washington.edu/~dbeyer