[BioC] Annotation using the affy package

James W. MacDonald jmacdon at uw.edu
Tue Oct 23 23:09:58 CEST 2012

Hi Jens,

On 10/23/2012 3:48 PM, Jens Lichtenberg [guest] wrote:
> 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():
> source("http://bioconductor.org/biocLite.R")
> library(affy)
> filenames<- c("1.CEL","2.CEL")
> affy.data<- ReadAffy(filenames = as.character(filenames))
> platform<- annotation(affy.data),".db"
> biocLite(platform)
> library(platform)
> 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)

ens <- select(mouse4302.db, featureNames(eset_pma), "ENSEMBL")

If all the probeset IDs in 'ens' and 'my_frame' match up, you can simply 
cbind() to my_frame. I assume they will, but I would check to be sure. 
Otherwise you can just merge().



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James W. MacDonald, M.S.
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

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