Hello,

I am now analyzing Affymetrix mouse 430_2 array, and need clarification for the following issues.

1) how to summarize the probe expression to the expression level of transcript/genes?
We are interested in the gene expression. I know that for human 1.0 ST gene array, we can use oligo package to get transcript expression. And for illumina array, there are only few probes designed for each gene, so we can only look at the probe level. For this mouse 430_2 array, there are usually 11 probes. I am thinking that using rma may not be enough.

2) and add annotation thereafter?
For the transcript level annotation, I have used the following code before. But not sure for this mouse array, is there a similar way or similar transcript database to do such? I know there is a database called mouse4302.db.
ID <- featureNames(geneCore2)
Symbol <- getSYMBOL(ID,"hugene10sttranscriptcluster.db")
fData(geneCore2) <- data.frame(ID=ID,Symbol=Symbol)

Any input would be very appreciated! Thank you very much in advance.

Thanks,
Xiayu

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