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

Cei Abreu-Goodger cei at sanger.ac.uk
Sun Jul 27 13:05:16 CEST 2008

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.



  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"]]
>> hgu95av2GO[["gnf1m2978_a_at"]]
> Please advice.
> - Gundala Viswanath
> Jakarta - Indonesia
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