text: user1430: I am learning about generating heatmaps using R. For this example I am using randomly generated data to test the process, but I encountered what appears to be an error or perhaps there is something am missing. Specifically, the values of Npy2r in groups A & B are the same, yet the heat map colors them differently. I am trying to understand why. Am including the R code I am using to generate the heat map
  heatmap.2(x, Rowv=F, Colv = F, scale="col", col=greenred(3), key=TRUE, symkey=FALSE,                             
        density.info="none",cexRow=1,cexCol=1,margins=c(6,11),  trace="none",srtCol=45)
  
  
  user1375: You have scale="col" in the code. What you are plotting is the z-score calculated based on the value distribution per column. Try changing it to "row" or "none".
  
original_text: 1430: <p>I am learning about generating heatmaps using R. For this example I am using randomly generated data to test the process, but I encountered what appears to be an error or perhaps there is something am missing. Specifically, the values of Npy2r in groups A &amp; B are the same, yet the heat map colors them differently. I am trying to understand why. Am including the R code I am using to generate the heat map<a href="https://i.stack.imgur.com/F9ToQ.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/F9ToQ.png" alt="heatmap"></a></p>
  
  <pre><code>heatmap.2(x, Rowv=F, Colv = F, scale="col", col=greenred(3), key=TRUE, symkey=FALSE,                             
        density.info="none",cexRow=1,cexCol=1,margins=c(6,11),  trace="none",srtCol=45)
  </code></pre>
   1375: <p>You have <code>scale="col"</code> in the code. What you are plotting is the z-score calculated based on the value distribution per column. Try changing it to <code>"row"</code> or <code>"none"</code>.</p>
  