[BioC] Annotating Results for HuEx 1.0 STv2 - Oligo

Atul atulkakrana at outlook.com
Thu Aug 29 05:40:55 CEST 2013

Hi All,

I am using Oligo package to analyse samples generated using HuEx 1.0 ST 
v2 chip. The problem I am facing is with annotating the results.

Here is my code (simplified):

celFilesA <- list.celfiles()
AF_data.A <- read.celfiles(celFilesA,pkgname='pd.huex.1.0.st.v2')
AF.eset.RMA <- rma(AF_data.A,target='core')

 > dim(exprs(AF.eset.RMA))
[1] 22011    10

##Attempt to annotate
ID <- rownames(AF.eset.RMA)
ensembl <- useMart('ensembl', dataset = 'hsapiens_gene_ensembl')
Anno <- 

 > dim(Anno)
[1] 1635    4

As you see, out of total 22011 genes/probeset I can annotate only 1635 
genes/probesets. Is there any way I can get the annotations for all of 
the genes/probesets and add them back to my expression set 
(AF.eset.RMA). So, that annotations are included in the final results.

Usually, with other chips I do this:
ID <- featureNames(AF.eset.RMA)
Symbol <- getSYMBOL(ID, 'mouse4302.db')
Name <- as.character(lookUp(ID, "mouse4302.db", "GENENAME"))
tmp <- data.frame(ID=ID, Symbol=Symbol, Name=Name,stringsAsFactors=F)
tmp[tmp=="NA"] <- NA
fData(AF.esetRMA) <- tmp

And this is what I want to achieve in present case. I would appreciate 
your help.



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