[BioC] Converting EnSeMBL Probe names into Gene Name

[James W. MacDonald]

Another alternative is to use the org.Hs.eg.db package

 > library(org.Hs.eg.db)
Loading required package: AnnotationDbi
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

   Vignettes contain introductory material. To view, type
   'openVignette()'. To cite Bioconductor, see
   'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: DBI
Loading required package: RSQLite
 > ens <- c("ENSG00000000003","ENSG00000000005","ENSG00000000419")
 > egs <- mget(ens, revmap(org.Hs.egENSEMBL))
 > egs
$ENSG00000000003
[1] "7105"

$ENSG00000000005
[1] "64102"

$ENSG00000000419
[1] "8813"

 > gns <- mget(unlist(egs), org.Hs.egSYMBOL)
 > gns
$`7105`
[1] "TSPAN6"

$`64102`
[1] "TNMD"

$`8813`
[1] "DPM1"

Since most BioC annotation packages are Entrez Gene-centric, you will 
need to map via the Entrez Gene ID, whereas you can do the direct 
mapping using biomaRt.

Best,

Jim

Sean Davis wrote:
> On Thu, Sep 18, 2008 at 4:37 AM, Gundala Viswanath <gundalav at gmail.com> wrote:
>> Dear all,
>>
>> Is there a way with Bioconductor in which I can
>> convert such EnSemBL probe names into the
>> standard gene names?
>>
>> AFFX-M27830_5_at
>> AFFX-M27830_M_at
>> ENSG00000000003_at
>> ENSG00000000005_at
>> ENSG00000000419_at
> 
> Hi, Gundala.  In general, you do not need to cross-post to both
> bioconductor and R lists.
> 
> These are not standard Ensembl names.  You could strip off the "_at"
> and some of them would become Ensembl gene names (the ones that begin
> with ENSG; the others look like affy control probes).  Then, you could
> use biomart to get information about them.  See the biomart vignette
> and help pages for assistance.
> 
> Sean
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Hildebrandt Lab
8220D MSRB III
1150 W. Medical Center Drive
Ann Arbor MI 48109-0646
734-936-8662