Body: <p>I need to identify differential genes across 8 groups. I know this can be done using DESeq2 or EdgeR as these are better suited and equipped.</p>
  
  <p>However, I was thinking if something like this piece of code could be tweaked. Here it works for two groups each with 3 replicates and generates a heatmap. The code is in R </p>
  
  <pre><code>pvals &lt;- apply(dm, 1, function(x) wilcox.test(x~c(rep(0,3), rep(1,9)))$p.value)
  heatmap(dm[pvals&lt;0.05,])
  </code></pre>
  
  <p>Thank you for your inputs and suggestions.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-08-14T15:11:36.677Z
Comments.Text: What is your reason not to use DESeq2 or EdgeR? Their models will work much better for RNAseq data than a simple Wilcoxon test.
Comments.UserDisplayName: PPK
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-08-14T20:06:15.817Z
Comments.Text: Welcome to Bioinformatics.SE! At the moment, your question simply asks "what about this?" while ignoring a tremendous amount of scholarship on differential expression analysis. Unless you can more clearly present a specific question or concern, there is a good chance this question will be closed as too broad or unclear.
Comments.UserDisplayName: Daniel Standage
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-08-16T15:26:36.487Z
Comments.Text: For a single measurement of some fixed, observable quantity like height or grades, using a Wilcoxon test isn't a bad idea. But RNA-seq is a very complicated system and can't simply be analyzed by something like a Wilcoxon test. Your results will be full of mistakes if you do this. I would recommend that you read some introduction to RNA-seq papers or textbooks and watch some presentations by Wolfgang Huber, Gordon Smyth, and Lior Pachter to see why this is the case
Comments.UserDisplayName: James Hawley
Tags: <r><rna-seq><differential-expression>
Title: Identification of differential genes across 8 groups
ThreadText: # Identification of differential genes across 8 groups
  
  (Asked by: username_0 on 2019-08-14)
  
  I need to identify differential genes across 8 groups. I know this can be done using DESeq2 or EdgeR as these are better suited and equipped.
  
  However, I was thinking if something like this piece of code could be tweaked. Here it works for two groups each with 3 replicates and generates a heatmap. The code is in R
  
  ```
  pvals <- apply(dm, 1, function(x) wilcox.test(x~c(rep(0,3), rep(1,9)))$p.value)
  heatmap(dm[pvals<0.05,])
  
  ```
  
  Thank you for your inputs and suggestions.
  
  **Tags:** r, rna-seq, differential-expression
  
  > **Comments:**
  > **username_1**: What is your reason not to use DESeq2 or EdgeR? Their models will work much better for RNAseq data than a simple Wilcoxon test.  
  > **username_2**: Welcome to Bioinformatics.SE! At the moment, your question simply asks "what about this?" while ignoring a tremendous amount of scholarship on differential expression analysis. Unless you can more clearly present a specific question or concern, there is a good chance this question will be closed as too broad or unclear.  
  > **username_3**: For a single measurement of some fixed, observable quantity like height or grades, using a Wilcoxon test isn't a bad idea. But RNA-seq is a very complicated system and can't simply be analyzed by something like a Wilcoxon test. Your results will be full of mistakes if you do this. I would recommend that you read some introduction to RNA-seq papers or textbooks and watch some presentations by Wolfgang Huber, Gordon Smyth, and Lior Pachter to see why this is the case  
  
  ---
  
  ## 0 answers
  
  