title: normal quantile transformation
body: <p>I need to do quantile normalization in R</p>
  
  <p>Input file  just a small subset I have over 5000 values:</p>
  
  <pre><code>x &lt;- data.frame(A =c(193973, 185750, 185511,NA), B= c(56433,52298, 53040, NA), C = c(4668, 6074,6246, NA))
  </code></pre>
  
  <p>software I am using is recommending</p>
  
  <pre><code>xtransformed = qqnorm(x, plot.it =F)$x
  </code></pre>
  
  <p>I don't understand "$x" here in the end ?</p>
  
  <p><strong>other question is:</strong></p>
  
  <p>if input is (which is my actual input</p>
  
  <pre><code>x &lt;- data.frame(A =c("A","B","C","D"), B = c("X", "Y", "Z","L"), C=c(193973, 185750, 185511, "NA"), D = c(56433,52298, 53040, "NA"), E = c(4668, 6074,6246, "NA"))
  </code></pre>
  
  <p>and I just select column I want to transform</p>
  
  <pre><code>y =x[,3:5]
  </code></pre>
  
  <p>Transformed it with that code and it doesnt work? What is the reason</p>
  
  <pre><code>ytransformed &lt;- qqnorm(y, plot.it =F)$y
  
  ytransformed 
  </code></pre>
  
  <p>I did that. Now I want to plot and see if it has transformed or not? how can I do that?</p>