Answers.Body: <p>The question isn't quite clear but you probably found a module that relates to your outcome and are talking about the module membership in that particular module. One possibility is that the module is downregulated in Experimental vs. Control in which case genes that are up in Experimental vs. Control would have a negative module membership simply because the module eigengene is negatively correlated with the numeric representation of Experimental vs. Control.</p>
  
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Answers.CreationDate: 2024-09-25T02:47:08.823Z
Answers.LastActivityDate: 2024-09-25T02:47:08.823Z
Answers.UserDisplayName: Peter Langfelder
Body: <p>I have data from a bulk RNA Tag-seq project I'm analyzing.</p>
  <p>Does it make sense that the signage (positive vs negative) of my logFC from DEseq2/limma is opposite to my gene signif. correlation/module membership from WGCNA? Or did I code them backwards during WGCNA?</p>
  <p>If my limma levels are Control, Experimental (ostensibly 0,1??) and for WGCNA I binarize my groups so that Control = 0 and Experimental = 1, why would the signage be opposite when comparing logFC and MM?</p>
  <p>For reference all of this work was done in R, if that matters.</p>
  <p>Thank you!!</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-09-24T23:33:02.703Z
Comments.Text: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.
Comments.UserDisplayName: Community
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-09-25T00:13:03.617Z
Comments.Text: Please show some of your results, e.g. the first few lines of the DESeq2 results table and the first few lines, subset to show the same genes.
Comments.UserDisplayName: gringer
Tags: <r><rna-seq><deseq2><limma><wgcna>
Title: Comparing DEseq/limma logFC in gene expression to gene signif. correlation/module membership from WGCNA -- sign problem?
ThreadText: # Comparing DEseq/limma logFC in gene expression to gene signif. correlation/module membership from WGCNA -- sign problem?
  
  (Asked by: username_0 on 2024-09-24)
  
  I have data from a bulk RNA Tag-seq project I'm analyzing.
  
  Does it make sense that the signage (positive vs negative) of my logFC from DEseq2/limma is opposite to my gene signif. correlation/module membership from WGCNA? Or did I code them backwards during WGCNA?
  
  If my limma levels are Control, Experimental (ostensibly 0,1??) and for WGCNA I binarize my groups so that Control = 0 and Experimental = 1, why would the signage be opposite when comparing logFC and MM?
  
  For reference all of this work was done in R, if that matters.
  
  Thank you!!
  
  **Tags:** r, rna-seq, deseq2, limma, wgcna
  
  > **Comments:**
  > **username_1**: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.  
  > **username_2**: Please show some of your results, e.g. the first few lines of the DESeq2 results table and the first few lines, subset to show the same genes.  
  
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  ## 1 answers
  
  ### Answer by username_3 on 2024-09-25. Score: 0
  
  The question isn't quite clear but you probably found a module that relates to your outcome and are talking about the module membership in that particular module. One possibility is that the module is downregulated in Experimental vs. Control in which case genes that are up in Experimental vs. Control would have a negative module membership simply because the module eigengene is negatively correlated with the numeric representation of Experimental vs. Control.
  
  
  ---
  
  