[BioC] Modifying annotation in Human Gene ST eset object
Javier Pérez Florido
jpflorido at gmail.com
Thu Nov 19 18:55:50 CET 2009
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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