Answers.Body: <p>You may be interested in reading up on heatmaps. For a history perspective (pre the biological introduction by <a href="http://www.pnas.org/content/95/25/14863" rel="nofollow noreferrer">Eisen et al.</a> ) read <em><a href="https://www.cs.uic.edu/~wilkinson/Publications/heatmap.pdf" rel="nofollow noreferrer">The History of the Cluster Heat Map</a></em> by Wilkinson and Friendly </p>
  
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Answers.CreationDate: 2018-07-31T12:16:23.250Z
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Answers.LastEditDate: 2018-07-31T22:13:24.550Z
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Answers.Body: <p>The dendrogram summarize the information of a group of values and sort them according to the similarity they have. It can be applied to both, samples and features.</p>
  
  <p>The dendrogram allows to visualize features that are more similar together, usually revealing patterns that wouldn't have been seen otherwise. </p>
  
  <p>In an article usually it is used something like: "we can see that X and Y are clustered together revealing that ... (they have something in common), while Z and A are clustered far"</p>
  
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Answers.CreationDate: 2018-07-30T07:43:35.940Z
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Answers.UserDisplayName: llrs
Body: <p>How to interpret heat map and dendrogram output for biological data (omics) in words (when writing results and discussion)?</p>
  
  <p>What should I consider (statistics behind?) and what is the best approach?</p>
  
  <p>Here is one of my HM for proteomics data.</p>
  
  <p>Script being used</p>
  
  <pre><code>col &lt;- colorRampPalette(c("red","yellow","darkgreen"))(30) 
  png("HM1.png")
  heatmap.2(as.matrix(df), Rowv = T, Colv = FALSE, dendrogram = "row", #scale = "row", col = col, density.info = "none", trace = "none", margins = c(7, 15) )
  dev.off()
  </code></pre>
  
  <p><a href="https://i.sstatic.net/FefR3.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/FefR3.png" alt="Heatmap output"></a>
  Heat Map output.</p>
  
  <p>I would be greatful if you would give an example.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-07-29T01:07:49.233Z
Comments.Text: Why are you producing the heatmap in the first place? What question are you trying to answer?
Comments.UserDisplayName: gringer
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-07-29T11:54:23.027Z
Comments.Text: Did you read the original paper on clustering by [Eisen et al. in 1998](http://www.pnas.org/content/95/25/14863)? What have you tried already to understand more about why other people use heatmap clustering?
Comments.UserDisplayName: benn
Tags: <r><clustering><proteomics>
Title: Omics data: How to interpret heatmap and dendrogram output?
ThreadText: # Omics data: How to interpret heatmap and dendrogram output?
  
  (Asked by: username_0 on 2018-07-28)
  
  How to interpret heat map and dendrogram output for biological data (omics) in words (when writing results and discussion)?
  
  What should I consider (statistics behind?) and what is the best approach?
  
  Here is one of my HM for proteomics data.
  
  Script being used
  
  ```
  col <- colorRampPalette(c("red","yellow","darkgreen"))(30) 
  png("HM1.png")
  heatmap.2(as.matrix(df), Rowv = T, Colv = FALSE, dendrogram = "row", #scale = "row", col = col, density.info = "none", trace = "none", margins = c(7, 15) )
  dev.off()
  
  ```
  
  [![Heatmap output](https://i.sstatic.net/FefR3.png)](https://i.sstatic.net/FefR3.png)
  Heat Map output.
  
  I would be greatful if you would give an example.
  
  **Tags:** r, clustering, proteomics
  
  > **Comments:**
  > **username_1**: Why are you producing the heatmap in the first place? What question are you trying to answer?  
  > **username_2**: Did you read the original paper on clustering by [Eisen et al. in 1998](http://www.pnas.org/content/95/25/14863)? What have you tried already to understand more about why other people use heatmap clustering?  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_4 on 2018-07-30. Score: 3 | Accepted answer
  
  The dendrogram summarize the information of a group of values and sort them according to the similarity they have. It can be applied to both, samples and features.
  
  The dendrogram allows to visualize features that are more similar together, usually revealing patterns that wouldn't have been seen otherwise.
  
  In an article usually it is used something like: "we can see that X and Y are clustered together revealing that ... (they have something in common), while Z and A are clustered far"
  
  
  ---
  
  ### Answer by username_3 on 2018-07-31. Score: 3
  
  You may be interested in reading up on heatmaps. For a history perspective (pre the biological introduction by [Eisen et al.](http://www.pnas.org/content/95/25/14863) ) read *[The History of the Cluster Heat Map](https://www.cs.uic.edu/~wilkinson/Publications/heatmap.pdf)* by Wilkinson and Friendly
  
  
  ---
  
  