[BioC] Modifying annotation in Human Gene ST eset object

Benilton Carvalho bcarvalh at jhsph.edu
Thu Nov 19 21:06:14 CET 2009


does

annotation(OligoEset) <- "hugene10sttranscriptcluster.db"

suffice?

b

On Nov 19, 2009, at 3:55 PM, Javier Pérez Florido wrote:

> Dear list,
> When normalizing CEL files from a Human Gene ST Array Experiment using
> oligo package, the eset object obtained makes use of pd.hugene. 
> 1.0.st.v1
> annotation package, but, AFAIK, EntrezID or other information cannot  
> be
> obtained using this annotation. Instead,  
> hugene10sttranscriptcluster.db
> annotation can be used for this purpose when summarizing to the gene  
> level.
>
> My question is, how can I modify the annotation package related to an
> eset object to allow the latter annotation file to be used together  
> with
> the eset object? For example, when creating a gene set collection  
> using
> GSEABase, the map from probe set IDs to PATH in KEGG is needed:
>
> library("GSEABase")
> gsc=GeneSetCollection(OligoEset,setType=KEGGCollection())
> Error in get(mapName, envir = pkgEnv, inherits = FALSE) :
>  object 'pd.hugene.1.0.st.v1PATH2PROBE' not found
>
> I would need to include hugene10sttranscriptcluster.db as annotation
> package in eset "OligoEset" to allow
> hugene10sttranscriptclusterPATH2PROBE to be used. How?
>
> Thanks,
> Javier
>
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