<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>

CC BY-SA 4.0
2021-09-01T22:35:14.163Z
Have you looked at the `oligo::rma` documentation? Can you clarify why this doesn't make sense to you?
Maximilian Press
<bioconductor><microarray>
Accessing expression data in an ExpressionSet
# Accessing expression data in an ExpressionSet

(Asked by: username_0 on 2021-09-01)

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

**Tags:** bioconductor, microarray
> **Comments:**
> **username_1**: Have you looked at the `oligo::rma` documentation? Can you clarify why this doesn't make sense to you?  

---

## 0 answers

