title: How to manipulate a count matrix from a DGEList?
body: <p>I am currently doing an RNASeq differential expression analysis. I used the function <code>DGEList</code> from <code>edgeR</code> to obtain the <code>count</code> and <code>sample</code> objects. I now want to remove a list of genes from <code>count</code>. This is the code I tried (with <code>remove</code> the list of genes I want to remove, <code>gene</code> the reference fo all genes I have):</p>
  
  <pre><code>n=0
  for (i in remove) {
      for (j in gene) {
          n=(n+1)
          if (i==j) {
              counts=counts[-n, ]
              n=(n-1)
          }
          if (n==nrow(counts)) {
              n=0
          }
      }
  }
  </code></pre>
  
  <p>I was expecting it to work as it does properly on a matrix that is similar.The code is still running while the one working on the matrix finished a long time ago. It should remove about 16000 rows.</p>
  
  <p>Do I have to manipulate it in a different way ? </p>