Answers.Body: <p>The answer is simply you use both sets of values in a one-way paired ANOVA. Note that certain criteria need to be in place for ANOVA, notably the Fmax test.</p>
  <p>Looking at the data 2-way ANOVA might be needed and that is more complicated, or else 2 one-way ANOVAs: I don't understand 'ctl2' and 'tube2' data. Is this a single or multiple drugs?</p>
  <p>Wilcoxon signed-rank test is the first choice test because there are no prior assumptions required, which replaces both the T-test and the 1-way ANOVA.</p>
  <p>Whatever you do, taking the mean and performing a T-test is not a good idea. You asked why ... because the variation between the values is critical to the significance of the test and is simply demonstrated:</p>
  <p>Tube 1 value</p>
  <pre><code>tube1 time X = 11
  tube1 time y = 9
  tube 1 mean = 10
  </code></pre>
  <p>Tube 2 value</p>
  <pre><code>tube 2 time x = 19
  tube 2 time y = 1
  tube 2 mean = 10
  </code></pre>
  <p>Thus both would appear to have no change - they are both 10 - and yet the variation between them means they observe very different behaviours. Thats why.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-05-14T16:37:49.737Z
Answers.LastActivityDate: 2022-05-14T16:47:35.557Z
Answers.LastEditDate: 2022-05-14T16:47:35.557Z
Answers.UserDisplayName: M__
Body: <p>I have duplicate drug efficacy experiments performed six months apart. I would like to know what is the right way to perform statistical analysis to understand fold changes after treatment with a drug.</p>
  <p>Say I have</p>
  <pre><code>ctrl1       tube1       ctrl2       tube2
  7,732637722 10,71639307 5,454318175 8,052899428
  6,69630905  8,762916793 7,441582994 9,855106201
  10,35624396 11,73716043 8,976524001 11,0975511
  4,29150392  4,848632578 5,901132154 7,918630661
  </code></pre>
  <p>and the same experiment but 6 months after (numbers are slightly different)</p>
  <p>Could I take the mean between samples divided by two can work out? If not - why?</p>
  <p>I would like to have statistically significant values for futher analysis.
  Thanks.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-05-14T02:53:55.480Z
Comments.Text: What do you want to show? Taking the mean is rarely a good move except in the final analysis
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-05-14T08:09:19.193Z
Comments.Text: I want to adjust values between the same experiments, to be able to analyze them via t-test for example. It's just these two batches are 6-months different.
Comments.UserDisplayName: Lara
Tags: <r><batch-effects>
Title: What is the best way to perform batch ajustment between two experiments?
ThreadText: # What is the best way to perform batch ajustment between two experiments?
  
  (Asked by: username_0 on 2022-05-13)
  
  I have duplicate drug efficacy experiments performed six months apart. I would like to know what is the right way to perform statistical analysis to understand fold changes after treatment with a drug.
  
  Say I have
  
  ```
  ctrl1       tube1       ctrl2       tube2
  7,732637722 10,71639307 5,454318175 8,052899428
  6,69630905  8,762916793 7,441582994 9,855106201
  10,35624396 11,73716043 8,976524001 11,0975511
  4,29150392  4,848632578 5,901132154 7,918630661
  
  ```
  
  and the same experiment but 6 months after (numbers are slightly different)
  
  Could I take the mean between samples divided by two can work out? If not - why?
  
  I would like to have statistically significant values for futher analysis.
  Thanks.
  
  **Tags:** r, batch-effects
  
  > **Comments:**
  > **username_1**: What do you want to show? Taking the mean is rarely a good move except in the final analysis  
  > **username_0**: I want to adjust values between the same experiments, to be able to analyze them via t-test for example. It's just these two batches are 6-months different.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2022-05-14. Score: 0
  
  The answer is simply you use both sets of values in a one-way paired ANOVA. Note that certain criteria need to be in place for ANOVA, notably the Fmax test.
  
  Looking at the data 2-way ANOVA might be needed and that is more complicated, or else 2 one-way ANOVAs: I don't understand 'ctl2' and 'tube2' data. Is this a single or multiple drugs?
  
  Wilcoxon signed-rank test is the first choice test because there are no prior assumptions required, which replaces both the T-test and the 1-way ANOVA.
  
  Whatever you do, taking the mean and performing a T-test is not a good idea. You asked why ... because the variation between the values is critical to the significance of the test and is simply demonstrated:
  
  Tube 1 value
  
  ```
  tube1 time X = 11
  tube1 time y = 9
  tube 1 mean = 10
  
  ```
  
  Tube 2 value
  
  ```
  tube 2 time x = 19
  tube 2 time y = 1
  tube 2 mean = 10
  
  ```
  
  Thus both would appear to have no change - they are both 10 - and yet the variation between them means they observe very different behaviours. Thats why.
  
  
  ---
  
  