Body: <p>I am conducting a meta-analysis of GWAS results for fecal gut microbiota across three different studies. Each study reports outcomes for the same general phenotype (e.g., Firmicutes abundances) but with slight variations in how the outcomes are defined. For instance, one study reports results for Firmicutes, while another study splits Firmicutes into subcategories such as Firmicutes_A, Firmicutes_B, and Firmicutes_C. The variation stems from differences in methodology.</p>
  <p>I am wondering if meta-analysis can be used to combine outcomes within the same study; then I can continue performing the actual meta-analysis between the diffent studies with (more) consistent features. Does the correlated data lead to bias narrowing confidence intervals and inflating type I error? Is there a better method to combine the outcomes? Thank you for the help in advance.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-11-21T18:04:26.190Z
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: 2024-11-21T19:08:50.357Z
Comments.Text: Basically yes you can. I will explain in detail later, but you might need to assess for bias between the data sets. Alternatively reprocessing the "Firmicutes" data set might be needed
Comments.UserDisplayName: M__
Tags: <gwas><metagenome><meta-analysis>
Title: Is Meta-Analysis Valid Method for Combining Outcomes within a Study
ThreadText: # Is Meta-Analysis Valid Method for Combining Outcomes within a Study
  
  (Asked by: username_0 on 2024-11-21)
  
  I am conducting a meta-analysis of GWAS results for fecal gut microbiota across three different studies. Each study reports outcomes for the same general phenotype (e.g., Firmicutes abundances) but with slight variations in how the outcomes are defined. For instance, one study reports results for Firmicutes, while another study splits Firmicutes into subcategories such as Firmicutes\_A, Firmicutes\_B, and Firmicutes\_C. The variation stems from differences in methodology.
  
  I am wondering if meta-analysis can be used to combine outcomes within the same study; then I can continue performing the actual meta-analysis between the diffent studies with (more) consistent features. Does the correlated data lead to bias narrowing confidence intervals and inflating type I error? Is there a better method to combine the outcomes? Thank you for the help in advance.
  
  **Tags:** gwas, metagenome, meta-analysis
  
  > **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**: Basically yes you can. I will explain in detail later, but you might need to assess for bias between the data sets. Alternatively reprocessing the "Firmicutes" data set might be needed  
  
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  ## 0 answers
  
  