text: user9788: I am using DESEQ2 for RNAseq analysis but i do not understand why I get this error.
  > dds <- DESeqDataSetFromMatrix(countData = data, 
  +                               colData = labeldata, 
  +                               design =~ subtype, tidy = TRUE)
  
  **Error** in `.rowNamesDF<-`(x, value = value) : 
    duplicate 'row.names' are not allowed
  
  I really do not know what is the issue. Could you please help?
  Thanks
  
  user9693: The hint is here:
  duplicate 'row.names' are not allowed
  rownames(data) should return a vector of only unique values, since it doesn't make sense to have the same gene/transcript in two different rows of your count matrix. How did you generate it?
  What does which(duplicated(rownames(data))) return? Maybe that'll give you a hint on what went wrong. In general, if you use salmon or kallisto for counting, you should use the excellent tximport package to get the counts into R, then create a DESeq dataset with DESeqDataSetFromTximport().
  EDITS:
  The replies to my answer prompted me to re-read your post and I saw that you had set tidy=TRUE, which means the duplicates are actually in your first column of your data.
  
original_text: 9788: <p>I am using DESEQ2 for RNAseq analysis but i do not understand why I get this error.</p>
  <pre><code>&gt; dds &lt;- DESeqDataSetFromMatrix(countData = data, 
  +                               colData = labeldata, 
  +                               design =~ subtype, tidy = TRUE)
  
  **Error** in `.rowNamesDF&lt;-`(x, value = value) : 
    duplicate 'row.names' are not allowed
  </code></pre>
  <p>I really do not know what is the issue. Could you please help?</p>
  <p>Thanks</p>
   9693: <p>The hint is here:</p>
  <p><code>duplicate 'row.names' are not allowed</code></p>
  <p><code>rownames(data)</code> should return a vector of only unique values, since it doesn't make sense to have the same gene/transcript in two different rows of your count matrix. How did you generate it?</p>
  <p>What does <code>which(duplicated(rownames(data)))</code> return? Maybe that'll give you a hint on what went wrong. In general, if you use <code>salmon</code> or <code>kallisto</code> for counting, you should use the excellent <code>tximport</code> package to get the counts into R, then create a DESeq dataset with <code>DESeqDataSetFromTximport()</code>.</p>
  <p>EDITS:</p>
  <p>The replies to my answer prompted me to re-read your post and I saw that you had set <code>tidy=TRUE</code>, which means the duplicates are actually in your first column of your <code>data</code>.</p>
  