[BioC] Assigning gene symbols to Affymetrix data and averaging probes

Hoyles, Lesley lesley.hoyles11 at imperial.ac.uk
Wed Oct 3 16:55:37 CEST 2012


I have processed my affy data and am able to annotate the object mice.loess using the following.
ID <- featureNames(mice.loess)
Symbol <- getSYMBOL(ID,'mouse4302.db')
fData(mice.loess) <- data.frame(ID=ID,Symbol=Symbol)

However, when I convert my object  as follows - expr.loess <- exprs(mice.loess) - I lose the annotation and have been unable to find a way to annotate expr.loess. Please could anybody suggest how I can annotate expr.loess?

Is there a way of averaging probes for each gene with Affymetrix data? I've been able to do this with single-channel Agilent data using the example given in the limma guide.

Thanks in advance for your help.

Best wishes

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