text: user1405: I have downloaded GSE16146 dataset from GEO using GEOquery R package. 
  I would like to extract "Data table" from downloaded GSE16146.  
  >library("GEOquery")
  >GSE16146 <- getGEO("GSE16146")
  >Table(GSE16146)[1:5,]
  
  This returns the following error:
  > Table(GSE16146)[1:5,]
  Error in (function (classes, fdef, mtable)  :
  unable to find an inherited method for function ‘Table’ for signature ‘"list"’
  
  Can anyone help?
  
  user294: According to the manual, all you need to do is: 
  library('GEOquery')
  gseGSE16146 <- getGEO('GSE16146', GSEMatrix=FALSE)
  
  As explanation, getGEO() outputs by default to GSEMatrix=TRUE and returns a list of ExpressionSet objects. You should get what you were looking for with: 
  Table(GSMList(gseGSE16146)[[1]])[1:5,]
  
  The manual has also a paragraph about this: 
  
  The GSE has  a  metadata section, just like the other classes. 
    However, it doesn’t have a GEODataTable.  Instead, it contains two
    lists, accessible using GPLList and GSMList, that are each lists of
    GPL and GSM objects.
  
  I tested the code I posted on R 3.3.2 and I get access to the Data Table just fine. 
  update: 
  Answering how to extract the actual expression data (not what asked in the original question): 
  library(GEOquery) 
  data = getGEO("GSE16146") 
  datExpr = exprs (data[[1]])
  
  
original_text: 1405: <p>I have downloaded <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE16146" rel="noreferrer">GSE16146</a> dataset from GEO using GEOquery R package. </p>
  
  <p>I would like to extract "Data table" from downloaded GSE16146.  </p>
  
  <pre><code>&gt;library("GEOquery")
  &gt;GSE16146 &lt;- getGEO("GSE16146")
  &gt;Table(GSE16146)[1:5,]
  </code></pre>
  
  <p>This returns the following error:</p>
  
  <pre><code>&gt; Table(GSE16146)[1:5,]
  Error in (function (classes, fdef, mtable)  :
  unable to find an inherited method for function ‘Table’ for signature ‘"list"’
  </code></pre>
  
  <p>Can anyone help?</p>
   294: <p>According to the <a href="https://www.bioconductor.org/help/course-materials/2011/BioC2011/LabStuff/publicDataTutorial.pdf" rel="nofollow noreferrer">manual</a>, all you need to do is: </p>
  
  <pre><code>library('GEOquery')
  gseGSE16146 &lt;- getGEO('GSE16146', GSEMatrix=FALSE)
  </code></pre>
  
  <p>As explanation, <code>getGEO()</code> outputs by default to <code>GSEMatrix=TRUE</code> and returns a list of <code>ExpressionSet</code> objects. You should get what you were looking for with: </p>
  
  <pre><code>Table(GSMList(gseGSE16146)[[1]])[1:5,]
  </code></pre>
  
  <p>The manual has also a paragraph about this: </p>
  
  <blockquote>
    <p>The GSE has  a  metadata section, just like the other classes. 
    However, it doesn’t have a GEODataTable.  Instead, it contains two
    lists, accessible using GPLList and GSMList, that are each lists of
    GPL and GSM objects.</p>
  </blockquote>
  
  <p>I tested the code I posted on <code>R 3.3.2</code> and I get access to the Data Table just fine. </p>
  
  <p>update: </p>
  
  <p>Answering how to extract the actual expression data (not what asked in the original question): </p>
  
  <pre><code>library(GEOquery) 
  data = getGEO("GSE16146") 
  datExpr = exprs (data[[1]])
  </code></pre>
  