Answers.Body: <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>
  
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Answers.Text: I know you now solved the issue, but I think you should double check the real [manual of GEOquery](http://bioconductor.org/packages/release/bioc/vignettes/GEOquery/inst/doc/GEOquery.html). But I think that the problem is with the type of data that is provided, I recall having downloaded this file with getGEOSuppFile
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Body: <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>
  
Tags: <microarray><geoquery>
Title: coexnet package for network co-expression analysis, is looking for a filelist.txt that doesn't exist
ThreadText: # coexnet package for network co-expression analysis, is looking for a filelist.txt that doesn't exist
  
  (Asked by: username_0 on 2018-02-27)
  
  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](https://www.bioconductor.org/packages/3.7/bioc/vignettes/coexnet/inst/doc/coexnet.pdf) 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](https://kasperdanielhansen.github.io/genbioconductor/html/GEOquery.html) 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?
  
  **Tags:** microarray, geoquery
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_0 on 2018-02-27. Score: 1 | Accepted answer
  
  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](https://ftp.ncbi.nlm.nih.gov/geo/series/GSE47nnn/GSE47010/suppl/)
  
  So there might be a problem at software side and they don't get downloaded.
  
  > **Comments:**
  > **username_1**: I know you now solved the issue, but I think you should double check the real [manual of GEOquery](http://bioconductor.org/packages/release/bioc/vignettes/GEOquery/inst/doc/GEOquery.html). But I think that the problem is with the type of data that is provided, I recall having downloaded this file with getGEOSuppFile  
  
  ---
  
  