[BioC] problem with IGH genes in org.Hs.egCHRLOC
mcarlson at fhcrc.org
Tue Nov 1 23:08:50 CET 2011
The CHRLOC mappings are based on the data from UCSC, but in order to
find a match to "28473", the UCSC knownToLocusLink table that we
download from UCSC every release has to have an entry in it for
"28473". Unfortunately, it doesn't. In fact, none of the NCBI linked
UCSC resources seems to have any entries for entrez gene "28473", which
means that you are probably stuck looking for this value by using
another resource (one that is not based on UCSC). So I think you really
do want to try biomart in this particular case.
On 10/31/2011 05:53 PM, Francois Pepin wrote:
> 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):
>  "IGHV1-3"
>  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.
> R version 2.13.1 (2011-07-08)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>  en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
> attached base packages:
>  stats graphics grDevices utils datasets methods base
> other attached packages:
>  org.Hs.eg.db_2.5.0 RSQLite_0.9-4 DBI_0.2-5
>  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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