[BioC] Annotation of Human Exon 1.0 ST

[Benilton Carvalho]

The contents of the Affymetrix annotation files are made available for you via:

netaffx = getNetAffx(geneSummaries, 'transcript')
pData(netaffx)[1:3, 1:2]

but you'll most likely need to parse the resulting data, as affymetrix
does not provide parsed files. :(

b


2013/5/18 Laura [guest] <guest at bioconductor.org>:
>
> 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
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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