Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-04-09T08:21:50.847Z
Answers.Text: Thank you. what package is DElist in?
Answers.UserDisplayName: holly
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-04-09T08:23:40.500Z
Answers.Text: That would be edgeR.
Answers.UserDisplayName: benn
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-04-09T08:31:09.270Z
Answers.Text: If I do:   ``````prac_count <- data.frame(prac_count, row.names=1), counts<- prac_count[,1], rownames(counts) <- prac_count[,1], DGE1 <-DGEList(counts) `````` If doesn't work... have I missed a step? Thank you so much
Answers.UserDisplayName: holly
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-04-09T08:48:04.480Z
Answers.Text: That's not the code I gave in my answer, is it?
Answers.UserDisplayName: benn
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-04-09T15:47:51.217Z
Answers.Text: Don't mention it! Good luck with it.
Answers.UserDisplayName: benn
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Answers.CreationDate: 2019-04-09T07:31:36.970Z
Answers.LastActivityDate: 2019-04-09T07:31:36.970Z
Answers.UserDisplayName: benn
Body: <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>
  
Tags: <r><limma>
Title: Voom transformation of RNA seq raw counts data
ThreadText: # Voom transformation of RNA seq raw counts data
  
  (Asked by: username_0 on 2019-04-08)
  
  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)
  
  ````````````
  
  ```
  
  **Tags:** r, limma
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2019-04-09. Score: 1 | Accepted answer
  
  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...
  
  > **Comments:**
  > **username_0**: Thank you. what package is DElist in?  
  > **username_1**: That would be edgeR.  
  > **username_0**: If I do:   ``````prac_count <- data.frame(prac_count, row.names=1), counts<- prac_count[,1], rownames(counts) <- prac_count[,1], DGE1 <-DGEList(counts) `````` If doesn't work... have I missed a step? Thank you so much  
  > **username_1**: That's not the code I gave in my answer, is it?  
  > **username_1**: Don't mention it! Good luck with it.  
  
  ---
  
  