text: user4398: I have RNA seq data of raw gene counts that I want to transform for linear modelling. I am trying to voom transform, to do a weighted analysis.
  Data frame: prac_count_10
  gene         S1     S2    S3   S4    S5 
  ENG0000456   0      1     10   145   24
  ENG0000458   7      2     9    0     0
  ENG0000657   76     12    56   10    2 
  ENG0000689   0      0     0    3     5
  
  
  Code:
  prac_prac_10 <- voom(prac_count_10[,2:5], design=NULL, lib.size=NULL, 
    normalize.method = "none", span = 0.5
  
  
  However this doesn't give an output with the gene sample names and logCPM values. Would like an output with gene id's and logCPM values for linear modelling.
  Also tried:
  cpm <- cpm(prac_count_10)
  lcpm <- cpm(prac_count_10, log=TRUE)
  
  
  ````````````
  
  
  user939: Try to use DElist() function before you transform, and also make rownames first.
  counts <- prac_count_10[,-1]
  
  rownames(counts) <- prac_count_10[,1]
  
  DGE1 <- DGEList(counts)
  
  And then continue with your voom...
  
original_text: 4398: <p>I have RNA seq data of raw gene counts that I want to transform for linear modelling. I am trying to voom transform, to do a weighted analysis.</p>
  
  <p>Data frame: prac_count_10</p>
  
  <pre><code>gene         S1     S2    S3   S4    S5 
  ENG0000456   0      1     10   145   24
  ENG0000458   7      2     9    0     0
  ENG0000657   76     12    56   10    2 
  ENG0000689   0      0     0    3     5
  
  </code></pre>
  
  <p>Code:</p>
  
  <pre><code>prac_prac_10 &lt;- voom(prac_count_10[,2:5], design=NULL, lib.size=NULL, 
    normalize.method = "none", span = 0.5
  
  </code></pre>
  
  <p>However this doesn't give an output with the gene sample names and logCPM values. Would like an output with gene id's and logCPM values for linear modelling.</p>
  
  <p>Also tried:</p>
  
  <pre><code>cpm &lt;- cpm(prac_count_10)
  lcpm &lt;- cpm(prac_count_10, log=TRUE)
  
  
  <span class="math-container">````````````</span>
  </code></pre>
   939: <p>Try to use <code>DElist()</code> function before you transform, and also make rownames first.</p>
  
  <pre><code>counts &lt;- prac_count_10[,-1]
  
  rownames(counts) &lt;- prac_count_10[,1]
  
  DGE1 &lt;- DGEList(counts)
  </code></pre>
  
  <p>And then continue with your voom...</p>
  