text: user14091: 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
  
  
  user-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.
  
original_text: 14091: <p>I used <code>rma</code> from the oligo package to normalize CEL files, returning an object of class <code>ExpressionSet</code>. How do I access the actual expression data?</p>
  <pre><code>&gt; data = read.celfiles(names)
  &gt; data2 = oligo::rma(data)
  class(data2)
  [1] &quot;ExpressionSet&quot;
  attr(,&quot;package&quot;)
  [1] &quot;Biobase&quot;
  &gt; data3 = as.matrix(data2)
  Error in as.vector(data) : 
    no method for coercing this S4 class to a vector
  </code></pre>
   -1: <p>The class of your object which the <code>rma</code> function returns is an <code>ExpressionSet</code> which is a standardized data structure in Bioconductor/R from the Biobase package.</p>
  <p>It stores both expression (a numeric matrix) data as well as column- and row annotation data.
  You have to use the getter function <code>exprs()</code> to access the expression data slot, so <code>exprs(data2)</code> which is then of class <code>matrix</code>, link to <a href="https://bioconductor.org/packages/release/bioc/vignettes/Biobase/inst/doc/ExpressionSetIntroduction.pdf" rel="nofollow noreferrer">documentation</a>.</p>
  