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

does annotation(OligoEset) <- "hugene10sttranscriptcluster.db" suffice? b On Nov 19, 2009, at 3:55 PM, Javier P?rez 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor