Accessing expression data in an ExpressionSet

Question

I used rma from the oligo package to normalize CEL files, returning an object of class ExpressionSet. How do I access the actual expression data?

> data = read.celfiles(names)
> data2 = oligo::rma(data)
class(data2)
[1] "ExpressionSet"
attr(,"package")
[1] "Biobase"
> data3 = as.matrix(data2)
Error in as.vector(data) : 
  no method for coercing this S4 class to a vector

Answer 1

The class of your object which the rma function returns is an ExpressionSet which is a standardized data structure in Bioconductor/R from the Biobase package.

It stores both expression (a numeric matrix) data as well as column- and row annotation data. You have to use the getter function exprs() to access the expression data slot, so exprs(data2) which is then of class matrix, link to documentation.