[BioC] Affymetrix HuGene 2.0 ST annotation

Natasha [guest] guest at bioconductor.org
Wed Jun 4 16:20:36 CEST 2014

Dear List,

I recently came across this post, that helped me in the analysis of data using this array. 

However, I am concerned about the annotation and wondered if what I get is usual for this kind of array.

eset_mat <- as.matrix(Eset)
dim(eset_mat) #53617     6


annodb <- "hugene20sttranscriptcluster.db"
ID     <- featureNames(Eset)
Symbol <- as.character(lookUp(ID, annodb, "SYMBOL"))
Name   <- as.character(lookUp(ID, annodb, "GENENAME"))
Entrez <- as.character(lookUp(ID, annodb, "ENTREZID"))
Ensembl <- as.character(lookUp(ID, annodb, "ENSEMBL"))

annot = data.frame("ID"=ID,"Symbol"=Symbol,"Description"=Name,"EntrezID"=Entrez,"EnsemblID"=Ensembl)

length(which(Symbol != "NA")) # 23672 =====> is this normal?
length(Symbol))  # 53617
Is it normal to get <50% annotation? 

(At present I have not done any filtering pre limma, used all 53K+ probes for DE).

Many Thanks,

 -- output of sessionInfo(): 


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