text: user8543: I have several mab files from medip-seq. they supposed to be replicates and I have to draw their correlation. First I used multiBamSummary from deeptools to merge all the bam files based on bi/bed. Now when I am using the plotCorrelation I do not get any file. the argument is :
  plotCorrelation --corData myMultiBamSumary.npz --corMethod spearman --whatToPlot scatterplot --skipZeros --removeOutliers --plotFile Myplot --plotFileFormat pdf
  
  Is that the correct strategy to pot the correlation? Is there any suggestion?
  Thanks alot
  
  user77: That's a completely normal way to plot correlation between them. Spearman correlation was a wise choice on your part, since it's rank based and you don't have to care as much about normalization.
  Update: It turns out that matplotlib is broken and I need to have a new deepTools release to work around that. That should be available sometime Sunday.
  
original_text: 8543: <p>I have several mab files from medip-seq. they supposed to be replicates and I have to draw their correlation. First I used multiBamSummary from deeptools to merge all the bam files based on bi/bed. Now when I am using the plotCorrelation I do not get any file. the argument is :</p>
  
  <pre><code>plotCorrelation --corData myMultiBamSumary.npz --corMethod spearman --whatToPlot scatterplot --skipZeros --removeOutliers --plotFile Myplot --plotFileFormat pdf
  </code></pre>
  
  <p>Is that the correct strategy to pot the correlation? Is there any suggestion?</p>
  
  <p>Thanks alot</p>
   77: <p>That's a completely normal way to plot correlation between them. Spearman correlation was a wise choice on your part, since it's rank based and you don't have to care as much about normalization.</p>
  
  <p>Update: It turns out that matplotlib is broken and I need to have a new deepTools release to work around that. That should be available sometime Sunday.</p>
  