text: user704: On my way to create a co-expression matrix for a microarray experiment, using the coexnet package I had to use a function called getAffy() which according to the packages' manual it :
  
  searches in your current or designated path file the folder with the
    GSE accession number and reads the filelist.txt file that contains the
    name of each GSM sample, in order to recognize them and join them in
    an unified AffyBatch object.
  
  So in some way, this file is needed to create the AffyBatch object. The thing here is that there is no such a file downloaded from the getInfo() function.
  Googling out the filelist.txt I reached only this result from GEOQuery manual, referring to that file. And as you can see there is a command in it eList2 <- getGEOSuppFiles("GSE11675") that is believed that it returns also the filelist.txt. I tried even with the example of the previously mentioned command, but no filelist.txt file ever fetched.
  Is there any way to setup my own filelist.txt file? Does anyone know what it contains and in what form?
  
  user704: Finally, I found it. filelist.txt file is accessible from the FTP server of the NCBI. For example for that specific microarray is stored here
  So there might be a problem at software side and they don't get downloaded.
  
original_text: 704: <p>On my way to create a co-expression matrix for a microarray experiment, using the <code>coexnet</code> package I had to use a function called <code>getAffy()</code> which according to the packages' <a href="https://www.bioconductor.org/packages/3.7/bioc/vignettes/coexnet/inst/doc/coexnet.pdf" rel="nofollow noreferrer">manual</a> it :</p>
  
  <blockquote>
    <p>searches in your current or designated path file the folder with the
    GSE accession number and reads the filelist.txt file that contains the
    name of each GSM sample, in order to recognize them and join them in
    an unified AffyBatch object.</p>
  </blockquote>
  
  <p>So in some way, this file is needed to create the AffyBatch object. The thing here is that there is no such a file downloaded from the <code>getInfo()</code> function.</p>
  
  <p>Googling out the <code>filelist.txt</code> I reached only this <a href="https://kasperdanielhansen.github.io/genbioconductor/html/GEOquery.html" rel="nofollow noreferrer">result</a> from GEOQuery manual, referring to that file. And as you can see there is a command in it <code>eList2 &lt;- getGEOSuppFiles("GSE11675")</code> that is believed that it returns also the filelist.txt. I tried even with the example of the previously mentioned command, but no filelist.txt file ever fetched.</p>
  
  <p>Is there any way to setup my own filelist.txt file? Does anyone know what it contains and in what form?</p>
   704: <p>Finally, I found it. <code>filelist.txt</code> file is accessible from the FTP server of the NCBI. For example for that specific microarray is stored <a href="https://ftp.ncbi.nlm.nih.gov/geo/series/GSE47nnn/GSE47010/suppl/" rel="nofollow noreferrer">here</a></p>
  
  <p>So there might be a problem at software side and they don't get downloaded.</p>
  