[BioC] Howto Get GO/Gene-names of GEO-Soft Probe-names

[Sean Davis]

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:
> library(AnnotationDbi)
>
> 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.

Sean

>  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).
>>
>> gnf1m29878_a_at
>> gnf1m13556_at
>> gnf1m09610_a_at
>> gnf1m11352_a_at
>> gnf1m26036_at
>> ...more...
>>
>> 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.
>>
>>> library("hgu95av2.db")
>>> hgu95av2SYMBOL[["gnf1m2978_a_at"]]
>>
>> NULL
>>>
>>> hgu95av2GO[["gnf1m2978_a_at"]]
>>
>> NULL
>>
>> Please advice.
>>
>> - Gundala Viswanath
>> Jakarta - Indonesia
>>
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>
>
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