R Expr IV: Annotation

The function fData() can extract feature data from your ExpressionSet objects.

1. Take a look at the head of the feature data from your normalized data set.

   head(fData(normData))

They are currently empty but you can get the row names with the function rownames(): head(rownames(fData(normData))). The row names tell you the names of the probes. They are not very informative, but currently this is all you know about the probes.

2. We will use the hgu95av2.dp package to add some gene names to the data. You will get the code here, but use the help files for the functions and try to understand what happens. You might need to make some small adjustments to the code

ID              <- featureNames(normData)
Symbol          <- getSYMBOL(ID, "hgu95av2.db")
fData(normData) <- data.frame(Symbol = Symbol)

3. Now use the fData() function together with the head() function again on your normalized data to see the the gene names of your first probes.

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