Hi all,
I have a bunch of probes identified from a mouse microarray experiment
that I want to get the equivalent human ortholog gene names (or
ensembl/entrez ID etc) for. I can't see any fields in the array
annotation database that will give me human homolog IDs - is there an
easy way to do this?
--
Cheers,
Nick Schurch
Data Analysis Group (The Barton Group),
School of Life Sciences,
University of Dundee,
Dow St,
Dundee,
DD1 5EH,
Scotland,
UK
Tel: +44 1382 388707
Fax: +44 1382 345 893
Hi Nick, the package annotationTools will help you find the human
orthologous gene IDs, based on a microarray-specific annotation file
and the
HomoloGene database, for instance. Applicable code examples are
provided in
the vignette.
Alexandre
> -----Original Message-----
> From: Nick Schurch [mailto:N.Schurch at dundee.ac.uk]
> Sent: Friday, April 30, 2010 9:14 AM
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] Annotation of orthologs
>
> Hi all,
>
> I have a bunch of probes identified from a mouse microarray
experiment
> that I want to get the equivalent human ortholog gene names (or
> ensembl/entrez ID etc) for. I can't see any fields in the array
> annotation database that will give me human homolog IDs - is there
an
> easy way to do this?
>
> --
> Cheers,
>
> Nick Schurch
>
> Data Analysis Group (The Barton Group),
> School of Life Sciences,
> University of Dundee,
> Dow St,
> Dundee,
> DD1 5EH,
> Scotland,
> UK
>
> Tel: +44 1382 388707
> Fax: +44 1382 345 893
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
Hi Nick,
this can be done with the biomaRt package. Have a look at the function
getLDS.
The vignette of biomaRt includes one example of using this function
(Task 11).
You may need to translate your probe identifiers to mouse entrezgene
or
Ensembl IDs in order to use this function.
Regards,
Joern
On Fri, 30 Apr 2010 14:14:11 +0100, Nick Schurch wrote
> Hi all,
>
> I have a bunch of probes identified from a mouse microarray
> experiment that I want to get the equivalent human ortholog gene
> names (or ensembl/entrez ID etc) for. I can't see any fields in the
array
> annotation database that will give me human homolog IDs - is there
an
> easy way to do this?
>
> --
> Cheers,
>
> Nick Schurch
>
>
---
Joern Toedling
Institut Curie -- U900
26 rue d'Ulm, 75005 Paris, FRANCE
Tel. +33 (0)156246927
Also see here:
http://article.gmane.org/gmane.science.biology.informatics.conductor/2
8014/match=inparanoid
Joern Toedling wrote:
> Hi Nick,
>
> this can be done with the biomaRt package. Have a look at the
function getLDS.
> The vignette of biomaRt includes one example of using this function
(Task 11).
> You may need to translate your probe identifiers to mouse entrezgene
or
> Ensembl IDs in order to use this function.
>
> Regards,
> Joern
>
> On Fri, 30 Apr 2010 14:14:11 +0100, Nick Schurch wrote
>> Hi all,
>>
>> I have a bunch of probes identified from a mouse microarray
>> experiment that I want to get the equivalent human ortholog gene
>> names (or ensembl/entrez ID etc) for. I can't see any fields in the
array
>> annotation database that will give me human homolog IDs - is there
an
>> easy way to do this?
>>
>> --
>> Cheers,
>>
>> Nick Schurch
>>
>>
>
> ---
> Joern Toedling
> Institut Curie -- U900
> 26 rue d'Ulm, 75005 Paris, FRANCE
> Tel. +33 (0)156246927
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor
--
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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