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[Bug]: Generating plots failing in DNA methylation QC #288

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m-kouhsar opened this issue Feb 3, 2025 · 0 comments · May be fixed by #289
Open

[Bug]: Generating plots failing in DNA methylation QC #288

m-kouhsar opened this issue Feb 3, 2025 · 0 comments · May be fixed by #289
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@m-kouhsar
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What happened?

If you run the QC.rmd script for some samples with only one Sentrix ID, some plots won't be generated dute the contrast issue in lm function. So, I think you need to check all columns in the projVar including Sentrix_ID, Sentrix_Position by remove_unwanted_columns function in line 112.

How can the bug be reproduced?

Simply by running the DNA methylation QC pipeline on some samples with the same Sentrix IDs.

Relevant log output


      		
    

      
  





        



            

              
            

        

      


      
    








      

    



      

  
            

    

      
    

    


      

          @m-kouhsar
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      fix: remove Sentrix_ID/Position if all values are the same
      #289
  



  

      
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      fix: remove Sentrix_ID/Position if all values are the same

    
      ejh243/BrainFANS
    





    
  




      

    

  
      

  

    

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