

Marc,

Thank you very much for the information. Does it mean that I have to use those acceptable "evidence code" to GOstats package or I can have my personal label? 

Thanks.

X.G.





Date: Tue, 22 Jan 2013 10:23:45 -0800
From: Marc Carlson <mcarlson@fhcrc.org>
To: bioconductor@r-project.org
Subject: Re: [BioC] question about "evidence code" in data.frame from
    GOstats packages with unsupported model organisms
Message-ID: <50FED931.60706@fhcrc.org>
Content-Type: text/plain

Hi,

The evidence codes are defined by the folks who work on GO, and it 
refers to the kind of evidence that supports applying a particular GO 
term to a specific gene ID.  For many genes to GO mappings in non-model 
organisms the association is "second hand", meaning that it was really 
studied on another organism and then assumed to also apply in this other 
organism (often because of sequence homology).

Here is a web site that lists some acceptable evidence codes:

http://www.geneontology.org/GO.evidence.shtml


Hope this helps,


   Marc




On 01/21/2013 09:07 AM, Fix Ace wrote:
> Just realized some typo in the subject of previous post. So would like to raise this question again since nobody answer it last time. This is relevant to usage of GOstat package with unsupported model organism.
>
> Thanks.
>
>
> ________________________________
>
> To: "bioconductor@r-project.org"<bioconductor@r-project.org>
> Sent: Wednesday, January 16, 2013 9:38 AM
> Subject: question about "evidence cole" in data.frame from GOstats packages with unsupported model organisms
>
>
> I am planning to use read.table to create the objects that feed to GOFrame. The manual says that the three columns are required, GO IDs, evidence code and gene IDs. I think I understand the first and third column, but what information should I put in evidence code?
>
> For example I have the following in text file:
> ---------------------------------
>
> GO:0002576    ***    gene1
>
> -------------------------------
>
> Does it work?
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>
>
>
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