[BioC] Annotation of Human Exon 1.0 ST

[Laura [guest]]

Hi list,

I am having trouble trying to annotate a Human Exon 1.0 ST expression set. I know little about R and bioconductor and I find it hard to understand the instructions I find on the web.

 When analyzing HGU 133 Plus 2.0 arrays, I just had to follow these instructions:
library("hgu133plus2.db")
symbol <- hgu133plus2SYMBOL
genename <- hgu133plus2GENENAME
symbols <- unlist(as.list(hgu133plus2SYMBOL))
genenames <- unlist(as.list(hgu133plus2GENENAME))
results <-  cbind(symbols,genenames,exprs.eset)
And the “results” would be the expression matrix with genenames and genesymbols associated to each affymetrix gene ID. I am trying to get the same results (the same matrix) for the Human Exon chip.

I have summarized my data to the gene level using the oligo package and created the expression matrix:

geneSummaries <- rma(abatch.raw, target="core")
expressionMatrix <- exprs (geneSummaries)

Now I understand that the best option is to use the biomaRt package to annotate, I have been reading the vignette but I am completely lost as for what I should do to just attach genenames, symbols, or some other identifier to the expression matrix. 

Could somebody tell me which commands or which steps I should follow?

Thank you very much

 -- output of sessionInfo(): 

no sessioninfo

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