title: cummeRbund Create Gene Set Error
body: <p>I am having trouble creating a Gene Set using cummeRbund (R software used to analyze cufflinks, cuffdiff output).</p>
  
  <p>I have been working from the cummeRbund manual that can be found <a href="http://compbio.mit.edu/cummeRbund/manual_2_0.html#tth_sEc7" rel="nofollow noreferrer">here</a> The directions have worked up until the point of creating the gene sets.</p>
  
  <p>Before creating the gene sets you need to create a vector of gene_ids to include. In the example they enclose each item in this list in quotation marks. I have a created a gene_ids .txt file named OtoSCOPE_v7_list_oneline.txt the first 4 entries in this list are shown below.</p>
  
  <pre><code>“Adcy1” “Bdp1” “Bsnd” “Cabp2”
  </code></pre>
  
  <p>Here is the create gene sets portion of the script that I have been using.</p>
  
  <pre><code>###################################
  # Creating Gene Sets
  ###################################
  #first created a vector of gene_ids that you want included in your gene set
  base_dir &lt;- "/Users/paulranum/Documents/cummeRbund"
  otoscope_genes &lt;- read.table(file.path(base_dir, "OtoSCOPE_v7_list_oneline.txt"), stringsAsFactors=FALSE)
  
  data(cuff)
  myGeneIds&lt;-otoscope_genes
  myGeneIds
  myGenes&lt;-getGenes(cuff, myGeneIds)
  myGenes
  </code></pre>
  
  <p>When I run this I get the following output and errors.</p>
  
  <pre><code>&gt; data(cuff)
  Warning message:
  In data(cuff) : data set 'cuff' not found
  &gt; myGeneIds&lt;-otoscope_genes
  &gt; myGeneIds
         V1     V2     V3      V4      
  1 “Adcy1” “Bdp1” “Bsnd” “Cabp2” 
  &gt; myGenes&lt;-getGenes(cuff, myGeneIds)
  Error in rsqlite_send_query(conn@ptr, statement) : 
    cannot start a transaction within a transaction
  &gt; myGenes
  Error: object 'myGenes' not found
  </code></pre>
  
  <p>From what I can tell there are two main issues going on.    </p>
  
  <ol>
  <li>it is not recognizing my data(cuff) command. cuff is the name of my CuffSet data file this file has worked for everything else. is this not the correct data file?   </li>
  <li>the error after the myGenes&lt;-getGenes(cuff, myGeneIds) command:</li>
  </ol>
  
  <blockquote>
    <p>Error in rsqlite_send_query(conn@ptr, statement) :  cannot start a
    transaction within a transaction</p>
  </blockquote>
  
  <p>Thanks for reading any help would be very much appreciated.</p>