Answers.Body: <p>Your question is not clear, you seem to mix the relevant terminology... </p>
  
  <p>First, you cannot run WGCNA for individual samples, only for individual conditions (with or without WT, depending on what question you're trying to answer and assuming you have enough samples in each condition). If that's what you have done, fine. The number of modules in each independent analysis will generally be different, that's because each condition is different. The module identification built into WGCNA as the default approach does not allow the user to specify the number of modules beforehand, but if you insist on getting a pre-specified number of modules, you could run WGCNA using the "manual" way (for example, Tutorial I, section 2b) and substitute another clustering method (e.g., PAM) that allows you to specify the number of clusters. You may find the results inferior though.</p>
  
  <p>Second, module preservation does not result in new modules. Module preservation evaluates whether modules found in data set A are preserved in a different data set B. To get new, common modules, you could run a consensus network analysis on pairs of conditions or all 3 conditions together. The number of modules you would find in a consensus analysis cannot be predicted from the number of modules you find in individual data sets. </p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-10-18T19:36:55.147Z
Answers.Text: "assuming you have enough samples in each condition)." sorry yes i mixed up and yes i have control have like 55 samples and treatment like 50 samples .Thank you for the clarification now it seems bit more clear I will read the tutorial a bit more
Answers.UserDisplayName: kcm
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-10-19T09:31:21.407Z
Answers.Text: Conceptual clarification I have done as I said Control sample WGCNA as well as treatment ones with numerous biological replicate .I get various modules and yes "umber of modules in each independent analysis will generally be different, that's because each condition is different." yes this is what i get .So if do module preservation analysis where I want to see if my "data set A are preserved in a different data set B" then the number of resulted module would be same as what I did WGCNA for Control sample where I would see w.r.t to my reference. Am I explaining it correctly ?
Answers.UserDisplayName: kcm
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-10-20T18:17:02.157Z
Answers.Text: Sorry, I still don't understand your question. Module preservation outputs, for each module in a reference network (A), preservation statistics of the module in a test network (B). Module preservation does not change the number of modules. Some modules from A may be preserved in B and some not; sometimes all modules are preserved, sometimes none of the modules are preserved. The number of modules from A that are preserved in B may be smaller or larger than the number of modules found in a separate network analysis of B.
Answers.UserDisplayName: Peter Langfelder
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-10-22T19:44:23.820Z
Answers.Text: Thank you for the clarification
Answers.UserDisplayName: kcm
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-10-18T17:27:36.977Z
Answers.LastActivityDate: 2019-10-18T17:27:36.977Z
Answers.UserDisplayName: Peter Langfelder
Body: <p>I have case control studies,4 different condition where I have 1 control and against which I'm have 3 comparisons to make.</p>
  
  <p>I did WGCNA for individuals samples .Here I have the kept the number of genes equal in all the cases .</p>
  
  <p>Now my question is whether the number of modules which are obtained from WGCNA would be similar in number if I run module preservation between two condition .</p>
  
  <p>Lets say i get 15 modules in Control condition and 16 treated condition if I run module preservation the number of modules which would come would be 15+16= 31 or its independent .</p>
  
  <p>The power I have kept same for both WGCNA and module preservation analysis. But Still I get different module numbers.</p>
  
  <p>Any suggestion would be highly appreciated </p>
  
Tags: <wgcna>
Title: WGCNA module preservation analysis
ThreadText: # WGCNA module preservation analysis
  
  (Asked by: username_0 on 2019-10-18)
  
  I have case control studies,4 different condition where I have 1 control and against which I'm have 3 comparisons to make.
  
  I did WGCNA for individuals samples .Here I have the kept the number of genes equal in all the cases .
  
  Now my question is whether the number of modules which are obtained from WGCNA would be similar in number if I run module preservation between two condition .
  
  Lets say i get 15 modules in Control condition and 16 treated condition if I run module preservation the number of modules which would come would be 15+16= 31 or its independent .
  
  The power I have kept same for both WGCNA and module preservation analysis. But Still I get different module numbers.
  
  Any suggestion would be highly appreciated
  
  **Tags:** wgcna
  
  
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  ## 1 answers
  
  ### Answer by username_1 on 2019-10-18. Score: 2 | Accepted answer
  
  Your question is not clear, you seem to mix the relevant terminology...
  
  First, you cannot run WGCNA for individual samples, only for individual conditions (with or without WT, depending on what question you're trying to answer and assuming you have enough samples in each condition). If that's what you have done, fine. The number of modules in each independent analysis will generally be different, that's because each condition is different. The module identification built into WGCNA as the default approach does not allow the user to specify the number of modules beforehand, but if you insist on getting a pre-specified number of modules, you could run WGCNA using the "manual" way (for example, Tutorial I, section 2b) and substitute another clustering method (e.g., PAM) that allows you to specify the number of clusters. You may find the results inferior though.
  
  Second, module preservation does not result in new modules. Module preservation evaluates whether modules found in data set A are preserved in a different data set B. To get new, common modules, you could run a consensus network analysis on pairs of conditions or all 3 conditions together. The number of modules you would find in a consensus analysis cannot be predicted from the number of modules you find in individual data sets.
  
  > **Comments:**
  > **username_0**: "assuming you have enough samples in each condition)." sorry yes i mixed up and yes i have control have like 55 samples and treatment like 50 samples .Thank you for the clarification now it seems bit more clear I will read the tutorial a bit more  
  > **username_0**: Conceptual clarification I have done as I said Control sample WGCNA as well as treatment ones with numerous biological replicate .I get various modules and yes "umber of modules in each independent analysis will generally be different, that's because each condition is different." yes this is what i get .So if do module preservation analysis where I want to see if my "data set A are preserved in a different data set B" then the number of resulted module would be same as what I did WGCNA for Control sample where I would see w.r.t to my reference. Am I explaining it correctly ?  
  > **username_1**: Sorry, I still don't understand your question. Module preservation outputs, for each module in a reference network (A), preservation statistics of the module in a test network (B). Module preservation does not change the number of modules. Some modules from A may be preserved in B and some not; sometimes all modules are preserved, sometimes none of the modules are preserved. The number of modules from A that are preserved in B may be smaller or larger than the number of modules found in a separate network analysis of B.  
  > **username_0**: Thank you for the clarification  
  
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