[BioC] Annotation using the affy package

Jens Lichtenberg [guest] guest at bioconductor.org
Tue Oct 23 21:48:56 CEST 2012

I am using the affy package to analyze a set of GSM files downloaded from GEO. In addition to providing a table with probe ids, expression levels and p values, I would like to have the ensembl ids associated with the probe ids.

I loaded in the corresponding platform data (in my case mouse4302) but I am not quite sure how to go about the connection of the data.

Here is the way I am building the analysis table:

 -- output of sessionInfo(): 


filenames <- c("1.CEL","2.CEL")

affy.data <- ReadAffy(filenames = as.character(filenames))
platform <- annotation(affy.data),".db"

eset_rma <- rma(affy.data)
eset_pma <- mas5calls(affy.data)
my_frame <- data.frame(exprs(eset_rma), assayDataElement(eset_pma, "se.exprs"))
my_frame <- my_frame[, sort(names(my_frame))]
write.table(my_frame, file="export.tsv", sep="\t", col.names = NA)

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