Dear Sean,

Apologies for the late reply. I tried biomaRt and again about 17% of the
ENSG ids are missing.

In the end, I uploaded the list to http://www.ensembl.org/biomart/ and got
all the IDs mapped. It appears that processed clone genes (e.g. AL161908.1,
RP11-492E3.2) were not included in the R package biomaRt or og.Hs.egENSEMBL.
Not ideal for future automation but OK for now.

Thank you.

Regards, Adai





Regards, Adai


On Fri, Oct 18, 2013 at 5:39 PM, Sean Davis <sdavis2@mail.nih.gov> wrote:

> On Fri, Oct 18, 2013 at 12:37 PM, Adaikalavan Ramasamy
> <adaikalavan.ramasamy@gmail.com> wrote:
> > Dear James,
> >
> > Thank you. This works brilliantly. However it now returns ENSG ids
> > (previously entrez IDs).
> >
> > When I try to map these into gene symbols using og.Hs.egENSEMBL, about
> 20%
> > of ENSG ids are not found. Should I use another database/package to do
> this
> > conversion?
>
> Hi, Adai.
>
> You might consider using the biomaRt package. ; )
>
> Sean
>

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