text: user285: The WGCNA analysis page48 of that link.
  In this analysis they are comparing the Preservation of modules between human and chimpanzee brain networks where i see the number of human modules and chimp modules are exact same in number as well as the color they are labeled.
  So is it necessary that two different condition where, Im comparing need to have equal number of modules to check the module preservation? Because the power would be different,then the downstream output would be different for two set of condition ,let say if Im trying to see what are the module conserved in my Control vs a disease condition ?
  I have 4 different condition such as CONTROL,BPD,SCZ and MDD all[micro-array expression data] brain disorder with samples number of 50,54,54,48.
  So what im trying to see is what are the modules are getting preseved in each diseased state when they are compared to Control condition.
  What i have done is I ran WGCNA on each condition separately and found what are the modules are there in different condition. So here I see the number of modules that are observed in each individual condition varies.
  Now if I do module preservation is it necessary to have similar number of modules from each condition ? Or its fine to have different module number from different condition and can still run the module preservation.
  These are gene expression network.
  Modules are obtained as explained in the WGCNA tutorial.
  Do you mean "conservation" or "preservation"? I mean module preservation 
  Suggestion would be highly appreciated 
  
  user851: The networks you want to compare do not have to have the same number of modules. (The human and chimp networks just happen to have the same number of modules.) In fact, you only need modules in the reference network; modules from the test network are not used at all and need not be defined. You may want to read the original article describing module preservation, it would help you understand how the method works, what it needs and what it does not.
  
original_text: 285: <p>The WGCNA analysis <a href="https://avesis.yildiz.edu.tr/resume/downloadfile/zeyneb?key=0936b44a-e367-4ed1-8f8b-cdf3cb4db7ae" rel="nofollow noreferrer">page48 of that link</a>.</p>
  
  <p>In this analysis they are comparing the Preservation of modules between human and chimpanzee brain networks where i see the number of human modules and chimp modules are exact same in number as well as the color they are labeled.</p>
  
  <p>So is it necessary that two different condition where, Im comparing need to have equal number of modules to check the module preservation? Because the power would be different,then the downstream output would be different for two set of condition ,let say if Im trying to see what are the module conserved in my Control vs a disease condition ?</p>
  
  <p>I have 4 different condition such as CONTROL,BPD,SCZ and MDD all[micro-array expression data] brain disorder with samples number of 50,54,54,48.</p>
  
  <p>So what im trying to see is what are the modules are getting preseved in each diseased state when they are compared to Control condition.</p>
  
  <p>What i have done is I ran WGCNA on each condition separately and found what are the modules are there in different condition. So here I see the number of modules that are observed in each individual condition varies.</p>
  
  <p>Now if I do module preservation is it necessary to have similar number of modules from each condition ? Or its fine to have different module number from different condition and can still run the module preservation.</p>
  
  <p>These are gene expression network.
  Modules are obtained as explained in the WGCNA tutorial.</p>
  
  <p><strong>Do you mean "conservation" or "preservation"?</strong> I mean module preservation </p>
  
  <p>Suggestion would be highly appreciated </p>
   851: <p>The networks you want to compare do not have to have the same number of modules. (The human and chimp networks just happen to have the same number of modules.) In fact, you only need modules in the reference network; modules from the test network are not used at all and need not be defined. You may want to read the original article describing module preservation, it would help you understand how the method works, what it needs and what it does not.</p>
  