[BioC] gene expression set using KEGG

[Martin Morgan]

On 11/21/2010 06:59 PM, Peevi Ijkl wrote:
> Hi List
> I performed qc on some data and then i did gcrma on the the raw data and 
> converted into an expression set object(data.m).i then performed filtering using 
> rowSds(data.f). Now I am trying to perform GeneSetCollection for KEGG but 
> getting the following error.
> 
>> gsc<-GeneSetCollection(data.f,setType= KEGGcollection)
> 
> Error: could not find function "KEGGcollection"
> Error in GeneSetCollection(data.f, setType = KEGGcollection()) : 
>   error in evaluating the argument 'setType' in selecting a method for function 
> 'GeneSetCollection'
> 
> 
> Please help

Hi peevi -- Capitalize 'Collection' in KEGGCollection, and use it as a
function KEGGCollection() as in the vignette (for GOCollection()) and
help page ?GeneSetCollection.

But it might help to understand where you are going -- following an
existing vignette (which?), or ??

martin

> peevi
> 
> 
>       
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> 
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