Answers.Body: <ol>
  <li>We cannot be sure about this. For all we know, they could have been sequenced to the same depth and there is a biological difference that drives the 1000x (ridiculously large) fold change.</li>
  <li>See above</li>
  </ol>
  
  <p>The only thing you can say for sure is that gene B is expressed twice as much as gene A in samples 1 and 2. That's what "relative" means - relative expression of genes within a sample.</p>
  
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Answers.Text: thanks this was helpful. just want to see what others have to say as well before I accept the answer
Answers.UserDisplayName: An Ignorant Wanderer
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Answers.Text: Oh of course. I’m no expert at this, but this is what I’ve encountered in our experiments.
Answers.UserDisplayName: Ram RS
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Answers.UserDisplayName: Ram RS
Answers.Body: <p>The process of RNA-seq is a sampling process of all the RNA molecules. We cannot make reliable comparisons before we know how deep we sample. And since we know it is a sample from a population, the absolute value does not make sense.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-06-13T14:38:44.350Z
Answers.Text: So can we know how deep we sample? And knowing that, what would that allow us to do exactly? And how does this tie to sequencing "depth"?
Answers.UserDisplayName: An Ignorant Wanderer
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Answers.Text: This is usually the sequencing depth when I think about this problem.
Answers.UserDisplayName: Phoenix Mu
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Body: <p>Let's say we have two samples, sample 1 and sample 2, and we're running an RNA seq experiment. Consider genes A and B for both. For simplicity, let's say that when we run the RNA seq experiment, we get the following results:</p>
  
  <p>gene A sample 1 count: 2</p>
  
  <p>gene B sample 1 count: 4</p>
  
  <p>gene A sample 2 count: 2000</p>
  
  <p>gene B sample 2 count: 4000</p>
  
  <p>Based on my understanding, RNA seq gives relative results. So I guess in this guess, how can you tell whether either one of the following are true:</p>
  
  <p>1- You sequenced sample 2 a thousand fold more compared to sample 1</p>
  
  <p>2- Sample 2 really has a thousand fold more expression in both genes A and B </p>
  
Tags: <rna-seq>
Title: Understanding the "relativeness" in RNA seq experiments
ThreadText: # Understanding the "relativeness" in RNA seq experiments
  
  (Asked by: username_0 on 2020-06-12)
  
  Let's say we have two samples, sample 1 and sample 2, and we're running an RNA seq experiment. Consider genes A and B for both. For simplicity, let's say that when we run the RNA seq experiment, we get the following results:
  
  gene A sample 1 count: 2
  
  gene B sample 1 count: 4
  
  gene A sample 2 count: 2000
  
  gene B sample 2 count: 4000
  
  Based on my understanding, RNA seq gives relative results. So I guess in this guess, how can you tell whether either one of the following are true:
  
  1- You sequenced sample 2 a thousand fold more compared to sample 1
  
  2- Sample 2 really has a thousand fold more expression in both genes A and B
  
  **Tags:** rna-seq
  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_1 on 2020-06-12. Score: 2 | Accepted answer
  
  1. We cannot be sure about this. For all we know, they could have been sequenced to the same depth and there is a biological difference that drives the 1000x (ridiculously large) fold change.
  2. See above
  
  The only thing you can say for sure is that gene B is expressed twice as much as gene A in samples 1 and 2. That's what "relative" means - relative expression of genes within a sample.
  
  > **Comments:**
  > **username_0**: thanks this was helpful. just want to see what others have to say as well before I accept the answer  
  > **username_1**: Oh of course. I’m no expert at this, but this is what I’ve encountered in our experiments.  
  
  ---
  
  ### Answer by username_2 on 2020-06-13. Score: 0
  
  The process of RNA-seq is a sampling process of all the RNA molecules. We cannot make reliable comparisons before we know how deep we sample. And since we know it is a sample from a population, the absolute value does not make sense.
  
  > **Comments:**
  > **username_0**: So can we know how deep we sample? And knowing that, what would that allow us to do exactly? And how does this tie to sequencing "depth"?  
  > **username_2**: This is usually the sequencing depth when I think about this problem.  
  
  ---
  
  