[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.
https://stat.ethz.ch/pipermail/bioconductor/2014-May/059408.html
However, I am concerned about the annotation and wondered if what I get is usual for this kind of array.
Code:
eset_mat <- as.matrix(Eset)
dim(eset_mat) #53617 6
library(annotate)
library(hugene20sttranscriptcluster.db)
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,
Natasha
-- output of sessionInfo():
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