[BioC] Howto Get GO/Gene-names of GEO-Soft Probe-names
sdavis2 at mail.nih.gov
Sun Jul 27 15:13:05 CEST 2008
On Sun, Jul 27, 2008 at 7:05 AM, Cei Abreu-Goodger <cei at sanger.ac.uk> wrote:
> Hi Gundala,
> Those probes are from the GNF mouse custom affymetrix array, and are as such
> not directly supported in bioconductor. But, you can easily construct an
> annotation package for this chip. Check out the vignette for SQLForge that
> comes with:
> You will need to prepare a text file with 2 columns, in the first the probe
> id and in the second a commonly used gene/transcript identifier such as
> Entrez, GeneBank, RefSeq... you can get this information directly from the
> NCBI or from the GNF website.
Just to add a bit here, the development branch of GEOquery includes a
flag to get the annotation GPL SOFT file for a GDS. The annotation
GPLs contain GO information for the probes, generally.
> On Sun, 27 Jul 2008, Gundala Viswanath wrote:
>> Dear all,
>> I have the following probe names selected from a dataset (GDS592),
>> taken from GEO (SOFT format).
>> And I want to get the GO term and Official Gene Name from these
>> probe names.
>> Is there a way to do it?
>> I tried these two Bioconductor commands but fail.
>> Please advice.
>> - Gundala Viswanath
>> Jakarta - Indonesia
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> Search the archives:
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