Answers.Body: <p>No, you can't get this from the data itself. If there is a control/reference sample on one channel, you need someone to annotate which channel it's on.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-01-21T01:20:47.073Z
Answers.LastActivityDate: 2021-01-21T01:20:47.073Z
Answers.UserDisplayName: user1799035
Body: <p>I'm sorry if this is a stupid question - I have not analysed two channel array data before.</p>
  <p>I have a GenePix data file, which does not seem to indicate which channel (red or green) is used as reference channel.</p>
  <p>If it possible to tell this from the data itself?</p>
  <p>Where raw is my data object, and G is a dataframe of the green channel data and R is the data frame of the red channel data, the ranges are as follows:</p>
  <pre><code>#range(raw<span class="math-container">$G)
  [1]    45 21939
  &gt; 
  &gt; range(raw$</span>R)
  [1]  39 332
  </code></pre>
  
Tags: <microarray>
Title: How to tell which channel is the reference channel in two channel (red green) array data?
ThreadText: # How to tell which channel is the reference channel in two channel (red green) array data?
  
  (Asked by: username_0 on 2021-01-18)
  
  I'm sorry if this is a stupid question - I have not analysed two channel array data before.
  
  I have a GenePix data file, which does not seem to indicate which channel (red or green) is used as reference channel.
  
  If it possible to tell this from the data itself?
  
  Where raw is my data object, and G is a dataframe of the green channel data and R is the data frame of the red channel data, the ranges are as follows:
  
  ```
  #range(raw$G)
  [1]    45 21939
  > 
  > range(raw$R)
  [1]  39 332
  
  ```
  
  **Tags:** microarray
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2021-01-21. Score: 2
  
  No, you can't get this from the data itself. If there is a control/reference sample on one channel, you need someone to annotate which channel it's on.
  
  
  ---
  
  