[BioC] Ensembl or Gencode version of TxDb.Hsapiens.UCSC.hg19.knownGene

[Sean Davis]

On Sun, Oct 27, 2013 at 6:51 PM, Adaikalavan Ramasamy
<adaikalavan.ramasamy at gmail.com> wrote:
> 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.

Hi, Adai.

The R biomaRt package actually queries the ensembl biomart, so they
two will give the same results if given the same query against the
same dataset.  Versions need to match, so that might be something to
check.

Sean


> Thank you.
>
> Regards, Adai
>
>
>
>
>
> Regards, Adai
>
>
> On Fri, Oct 18, 2013 at 5:39 PM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
>
>> On Fri, Oct 18, 2013 at 12:37 PM, Adaikalavan Ramasamy
>> <adaikalavan.ramasamy at 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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