[BioC] problem with IGH genes in org.Hs.egCHRLOC

Francois Pepin francois.pepin at sequentainc.com
Tue Nov 1 01:53:12 CET 2011

Hi everyone,

I'm trying to get information about the IGH alleles and i'm getting strange results from org.Hs.eg.db.

For example, if we use IGHV1-3 (located at chr14, starting around 106,471,246 on NCBI & Ensembl websites):

> library(org.Hs.eg.db)
> get("28473",org.Hs.egSYMBOL)
[1] "IGHV1-3"
> get("28473",org.Hs.egCHRLOC)
[1] NA

I guess I could use biomart for these, but I'm surprised that org.Hs.egCHRLOC would not work for these genes. A quick test with other genes show results that are consistent with the data on the NCBI & Ensembl websites. I've also tested it on the devel version downloaded today (org.Hs.eg.db_2.5.0) with the same results.

> sessionInfo()
R version 2.13.1 (2011-07-08)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] org.Hs.eg.db_2.5.0   RSQLite_0.9-4        DBI_0.2-5           
[4] AnnotationDbi_1.14.1 Biobase_2.12.2      

François Pepin
Sequenta, Inc.
400 E. Jamie Court, Suite 301
South San Francisco, CA 94080
650 243 3929 p
francois.pepin at sequentainc.com
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