Extracting expression data from GSE dataset downloaded from GEO I have downloaded GSE16146 dataset from GEO using GEOquery R package. 

I would like to extract "Data table" from downloaded GSE16146.  

&gt;library("GEOquery")
&gt;GSE16146 &lt;- getGEO("GSE16146")
&gt;Table(GSE16146)[1:5,]


This returns the following error:

&gt; 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?
According to the manual, all you need to do is: 

library('GEOquery')
gseGSE16146 &lt;- 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]])